############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RBGL_1.70.0.tar.gz && rm -rf RBGL.buildbin-libdir && mkdir RBGL.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RBGL.buildbin-libdir RBGL_1.70.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RBGL_1.70.0.zip && rm RBGL_1.70.0.tar.gz RBGL_1.70.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 52 1963k 52 1039k 0 0 1039k 0 0:00:01 0:00:01 --:--:-- 1039k 100 1963k 100 1963k 0 0 1295k 0 0:00:01 0:00:01 --:--:-- 1296k install for i386 * installing *source* package 'RBGL' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bbc.cpp -o bbc.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cliques.cpp -o cliques.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c clusteringCoef.cpp -o clusteringCoef.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clusteringCoef.cpp: In function 'SEXPREC* graphGenerator(SEXP, SEXP, SEXP)': clusteringCoef.cpp:394:40: warning: 'u' may be used uninitialized in this function [-Wmaybe-uninitialized] Graph_ud::vertex_descriptor v, u, w=Graph_ud::null_vertex(); ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dominatorTree.cpp -o dominatorTree.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from edmonds_optimum_branching.hpp:94, from edmonds_optimum_branching.cpp:3: edmonds_optimum_branching_impl.hpp: In function 'void edmonds_optimum_branching(TEdgeListGraph&, TVertexIndexMap, TWeightMap, TInputIterator, TInputIterator, TOutputIterator)': edmonds_optimum_branching_impl.hpp:520:71: warning: typedef 'EdgeIter' locally defined but not used [-Wunused-local-typedefs] typedef typename graph_traits::edge_iterator EdgeIter; ^~~~~~~~ edmonds_optimum_branching_impl.hpp:521:71: warning: typedef 'weight_t' locally defined but not used [-Wunused-local-typedefs] typedef typename property_traits::value_type weight_t; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hcs.cpp -o hcs.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from mincut.hpp:4, from hcs.cpp:2: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function 'typename boost::graph_traits::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = const R_adjacency_list; OutputIterator = std::back_insert_iterator >]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] typename Traits::vertex_descriptor p; ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c incrConnComp.cpp -o incrConnComp.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from incrConnComp.cpp:2: incrConnComp.cpp: In function 'SEXPREC* BGL_incr_comp_internal(SEXP, SEXP, SEXP, E_IC_METHOD)': incrConnComp.cpp:74:32: warning: unused variable 'child_index' [-Wunused-variable] BOOST_FOREACH(VertexIndex child_index, components[current_index]) { ^~~~~~~~~~~ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:1114:14: note: in definition of macro 'BOOST_FOREACH' for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true) ^~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c interfaces.cpp -o interfaces.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_tsort_D(SEXP, SEXP, SEXP)': interfaces.cpp:81:17: warning: catching polymorphic type 'struct boost::not_a_dag' by value [-Wcatch-value=] catch ( not_a_dag ) ^~~~~~~~~ interfaces.cpp:57:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^~~~ interfaces.cpp:61:62: warning: typedef 'Color' locally defined but not used [-Wunused-local-typedefs] typedef property_map::type Color; ^~~~~ interfaces.cpp: In function 'SEXPREC* BGL_bfs_D(SEXP, SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:98:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^~~~ interfaces.cpp:99:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; ^~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_dfs_D(SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:142:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^~~~ interfaces.cpp:143:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; ^~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_connected_components_U(SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:198:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::edge_descriptor Edge; ^~~~ interfaces.cpp:199:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; ^~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_strong_components_D(SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:225:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^~~~ interfaces.cpp:226:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; ^~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_biconnected_components_U(SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:252:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::edge_descriptor Edge; ^~~~ interfaces.cpp:253:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; ^~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_articulation_points_U(SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:295:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::edge_descriptor Edge; ^~~~ interfaces.cpp: In function 'SEXPREC* BGL_edge_connectivity_U(SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:320:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; ^~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_sequential_vertex_coloring(SEXP, SEXP, SEXP)': interfaces.cpp:360:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::edge_descriptor Edge; ^~~~ interfaces.cpp:361:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; ^~~~~~ In file included from interfaces.cpp:7: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function 'typename boost::graph_traits::degree_size_type boost::edge_connectivity(VertexListGraph&, OutputIterator) [with VertexListGraph = R_adjacency_list; OutputIterator = std::back_insert_iterator > >]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] typename Traits::vertex_descriptor p; ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c minST.cpp -o minST.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ minST.cpp: In function 'SEXPREC* BGL_KMST_D(SEXP, SEXP, SEXP, SEXP)': minST.cpp:14:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; ^~~~~~ minST.cpp: In function 'SEXPREC* BGL_KMST_U(SEXP, SEXP, SEXP, SEXP)': minST.cpp:48:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; ^~~~~~ minST.cpp: In function 'SEXPREC* BGL_PRIM_U(SEXP, SEXP, SEXP, SEXP)': minST.cpp:81:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::edge_descriptor Edge; ^~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'void boost::detail::kruskal_mst_impl(const Graph&, OutputIterator, Rank, Parent, Weight) [with Graph = R_adjacency_list; OutputIterator = std::back_insert_iterator > >; Rank = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, unsigned int>, unsigned int, unsigned int&>; Parent = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, unsigned int>, unsigned int, unsigned int&>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& ei +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from minST.cpp:2: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:55: note: '*((void*)& ei +24)' was declared here typename graph_traits< Graph >::edge_iterator ei, eiend; ^~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:32, from RBGL.hpp:38, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/edge.hpp:27:71: warning: '*((void*)(& ei)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized] inline edge_base(Vertex s, Vertex d) : m_source(s), m_target(d) {} ^ In file included from minST.cpp:2: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:55: note: '*((void*)(& ei)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' was declared here typename graph_traits< Graph >::edge_iterator ei, eiend; ^~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mincut.cpp -o mincut.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'SEXPREC* BGL_max_flow_internal(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, E_MF_METHOD)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& ei +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ mincut.cpp:99:19: note: '*((void*)& ei +24)' was declared here edge_iterator ei, e_end; ^~ mincut.cpp:103:41: warning: '*((void*)(& ei)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > > > >*, std::vector > > > >, std::allocator > > > > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(eList)[i++] = source(*ei, flow_g); ~~~~~~^~~~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:148:48: warning: '*((void*)(& ei)+16).__gnu_cxx::__normal_iterator > > > >*, std::vector > > > >, std::allocator > > > > > > >::_M_current' may be used uninitialized in this function [-Wmaybe-uninitialized] &(*this->base()).get_property()); ^ mincut.cpp:99:19: note: '*((void*)(& ei)+16).__gnu_cxx::__normal_iterator > > > >*, std::vector > > > >, std::allocator > > > > > > >::_M_current' was declared here edge_iterator ei, e_end; ^~ In file included from mincut.hpp:4, from mincut.cpp:2: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function 'typename boost::graph_traits::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = R_adjacency_list; OutputIterator = std::back_insert_iterator >]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] typename Traits::vertex_descriptor p; ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ordering.cpp -o ordering.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/king_ordering.hpp:18, from ordering.cpp:9: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ordering.cpp: In function 'SEXPREC* BGL_min_degree_ordering(SEXP, SEXP, SEXP, SEXP)': ordering.cpp:133:53: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits::vertex_descriptor Vertex; ^~~~~~ ordering.cpp: In function 'SEXPREC* BGL_king_ordering(SEXP, SEXP, SEXP, SEXP)': ordering.cpp:182:48: warning: variable 'id' set but not used [-Wunused-but-set-variable] property_map::type id = get(vertex_index, g); ^~ ordering.cpp:176:53: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits::vertex_descriptor Vertex; ^~~~~~ ordering.cpp: In function 'SEXPREC* BGL_sloan_ordering(SEXP, SEXP, SEXP, SEXP, SEXP)': ordering.cpp:232:47: warning: typedef 'Pair' locally defined but not used [-Wunused-local-typedefs] typedef std::pair Pair; ^~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c planar.cpp -o planar.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ planar.cpp: In function 'SEXPREC* planarFaceTraversal(SEXP, SEXP, SEXP)': planar.cpp:161:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i = 0; i < v_vis.f_vis.size(); i++ ) ~~^~~~~~~~~~~~~~~~~~~~ planar.cpp:165:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int j = 0; j < v_vis.f_vis[i].size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~~ planar.cpp: In function 'SEXPREC* planarCanonicalOrdering(SEXP, SEXP, SEXP)': planar.cpp:256:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i = 0; i < ordering.size(); i++ ) ~~^~~~~~~~~~~~~~~~~ planar.cpp:225:34: warning: variable 'oi_end' set but not used [-Wunused-but-set-variable] Vertex_Vec_t::iterator oi, oi_end = ordering.end(); ^~~~~~ planar.cpp: In function 'SEXPREC* isStraightLineDrawing(SEXP, SEXP, SEXP, SEXP)': planar.cpp:369:28: warning: comparison of integer expressions of different signedness: 'int' and 'boost::detail::adj_list_gen, boost::property >, boost::vecS, boost::vecS, boost::undirectedS, boost::property, boost::property, boost::no_property, boost::listS>::config::vertices_size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i = 0, j = 0; i < num_vertices(g); i++ ) ~~^~~~~~~~~~~~~~~~~ planar.cpp: In function 'SEXPREC* isKuratowskiSubgraph(SEXP, SEXP, SEXP)': planar.cpp:429:36: warning: variable 'ki_end' set but not used [-Wunused-but-set-variable] Edge_Vec_t::iterator ki, ki_end = kuratowski_edges.end(); ^~~~~~ planar.cpp:461:6: warning: unused variable 'i' [-Wunused-variable] int i, j = 0; ^ In file included from planar.cpp:6: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/chrobak_payne_drawing.hpp: In function 'void boost::chrobak_payne_straight_line_drawing(const Graph&, PlanarEmbedding, ForwardIterator, ForwardIterator, GridPositionMap, VertexIndexMap) [with Graph = boost::adjacency_list, boost::property >; PlanarEmbedding = boost::iterator_property_map<__gnu_cxx::__normal_iterator >*, std::vector > > >, boost::vec_adj_list_vertex_id_map, unsigned int> >; ForwardIterator = __gnu_cxx::__normal_iterator >; GridPositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, unsigned int> >; VertexIndexMap = boost::vec_adj_list_vertex_id_map, unsigned int>]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/chrobak_payne_drawing.hpp:207:22: warning: 'next_to_rightmost' may be used uninitialized in this function [-Wmaybe-uninitialized] vertex_t next_to_rightmost; ^~~~~~~~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12, from planar.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp: In member function 'void boost::boyer_myrvold_impl::extract_kuratowski_subgraph(OutputIterator, EdgeIndexMap) [with OutputIterator = std::back_insert_iterator > >; EdgeIndexMap = boost::adj_list_edge_property_map, boost::edge_index_t>; Graph = boost::adjacency_list, boost::property >; VertexIndexMap = boost::vec_adj_list_vertex_id_map, unsigned int>; StoreOldHandlesPolicy = boost::graph::detail::store_old_handles; StoreEmbeddingPolicy = boost::graph::detail::no_embedding]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1264:9: warning: 'bicomp_root' may be used uninitialized in this function [-Wmaybe-uninitialized] if (bicomp_root != v) ^~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:19, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12, from planar.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/named_function_params.hpp: In static member function 'static bool boost::maximum_cardinality_matching_verifier::verify_matching(const Graph&, MateMap, VertexIndexMap) [with Graph = R_adjacency_list; MateMap = unsigned int*; VertexIndexMap = boost::vec_adj_list_vertex_id_map, unsigned int>]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:192:64: warning: '*((void*)& occ +8)' may be used uninitialized in this function [-Wmaybe-uninitialized] bgl_named_params(T v, const Base& b) : m_value(v), m_base(b) {} ^ In file included from planar.cpp:11: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/max_cardinality_matching.hpp:778:52: note: '*((void*)& occ +8)' was declared here detail::odd_components_counter< v_size_t > occ(num_odd_components); ^~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c registerSigHandlers.cpp -o registerSigHandlers.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c shortestPath.cpp -o shortestPath.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ shortestPath.cpp: In function 'SEXPREC* BGL_dijkstra_shortest_paths_D(SEXP, SEXP, SEXP, SEXP, SEXP)': shortestPath.cpp:17:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^~~~ shortestPath.cpp: In function 'SEXPREC* BGL_dag_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)': shortestPath.cpp:136:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^~~~ shortestPath.cpp: In function 'SEXPREC* BGL_floyd_warshall_all_pairs_shortest_paths_D(SEXP, SEXP, SEXP, SEXP)': shortestPath.cpp:177:81: warning: typedef 'Graph' locally defined but not used [-Wunused-local-typedefs] property< edge_weight_t, double, property< edge_weight2_t, double > > > Graph; ^~~~~ shortestPath.cpp:180:39: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef std::pair < int, int >Edge; ^~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list, boost::property >, boost::no_property, boost::listS>; Size = unsigned int; WeightMap = boost::adj_list_edge_property_map >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& i +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28, from shortestPath.cpp:4: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: '*((void*)& i +24)' was declared here typename GTraits::edge_iterator i, end; ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: warning: '*((void*)(& i)+16).__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >::_M_current' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list >; Size = int; WeightMap = boost::adj_list_edge_property_map, boost::edge_weight_t>; PredecessorMap = unsigned int*; DistanceMap = double*; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& i +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28, from shortestPath.cpp:4: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: '*((void*)& i +24)' was declared here typename GTraits::edge_iterator i, end; ^ In file included from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:129:65: warning: '*((void*)(& i)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized] inline const T& get(const T* pa, std::ptrdiff_t k) { return pa[k]; } ~~^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28, from shortestPath.cpp:4: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: '*((void*)(& i)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' was declared here typename GTraits::edge_iterator i, end; ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: warning: '*((void*)(& i)+16).__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >::_M_current' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::floyd_warshall_all_pairs_shortest_paths(const VertexAndEdgeListGraph&, DistanceMatrix&, const WeightMap&, const BinaryPredicate&, const BinaryFunction&, const Infinity&, const Zero&) [with VertexAndEdgeListGraph = R_adjacency_list; DistanceMatrix = Basic2DMatrix; WeightMap = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; Zero = double]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& first +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from shortestPath.cpp:7: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:101:68: note: '*((void*)& first +24)' was declared here typename graph_traits< VertexAndEdgeListGraph >::edge_iterator first, last; ^~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'SEXPREC* BGL_bellman_ford_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& ei +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ shortestPath.cpp:101:50: note: '*((void*)& ei +24)' was declared here graph_traits< EdgeGraph >::edge_iterator ei, ei_end; ^~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list; DistanceMatrix = Basic2DMatrix; VertexID = boost::vec_adj_list_vertex_id_map, unsigned int>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; DistanceZero = double]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& e +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from shortestPath.cpp:4: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: '*((void*)& e +24)' was declared here typename Traits2::edge_iterator e, e_end; ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_array.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/d_ary_heap.hpp:20, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/dijkstra_shortest_paths.hpp:20, from shortestPath.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_array.hpp:201:18: warning: '*((void*)(& e)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized] return px[i]; ~~^ In file included from shortestPath.cpp:4: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: '*((void*)(& e)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' was declared here typename Traits2::edge_iterator e, e_end; ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& e +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from shortestPath.cpp:4: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:84:41: note: '*((void*)& e +24)' was declared here typename Traits1::edge_iterator e, e_end; ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:89:41: warning: '*((void*)(& e)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized] boost::tie(e2, z) = add_edge( ~~~~~~~~^ get(id1, source(*e, g1)) + 1, get(id1, target(*e, g1)) + 1, g2); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sna.cpp -o sna.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ sna.cpp: In function 'SEXPREC* lambdaSets(SEXP, SEXP, SEXP, SEXP)': sna.cpp:161:9: warning: variable 'res_cap' set but not used [-Wunused-but-set-variable] res_cap = get(edge_residual_capacity, flow_g); ^~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list, boost::property >, boost::no_property, boost::listS>; Size = unsigned int; WeightMap = boost::adj_list_edge_property_map >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& i +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28, from sna.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: '*((void*)& i +24)' was declared here typename GTraits::edge_iterator i, end; ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: warning: '*((void*)(& i)+16).__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >::_M_current' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list; DistanceMatrix = Basic2DMatrix; VertexID = boost::vec_adj_list_vertex_id_map, unsigned int>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; DistanceZero = double]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& e +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from sna.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: '*((void*)& e +24)' was declared here typename Traits2::edge_iterator e, e_end; ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/shared_array_property_map.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:27, from sna.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_array.hpp:201:18: warning: '*((void*)(& e)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized] return px[i]; ~~^ In file included from sna.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: '*((void*)(& e)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' was declared here typename Traits2::edge_iterator e, e_end; ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: warning: '*((void*)(& e)+16).__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >::_M_current' may be used uninitialized in this function [-Wmaybe-uninitialized] "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c transitive_closure.cpp -o transitive_closure.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'SEXPREC* BGL_transitive_closure_D(SEXP, SEXP, SEXP)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& ei +24)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ transitive_closure.cpp:43:33: note: '*((void*)& ei +24)' was declared here Graph_dd::edge_iterator ei, e_end; ^~ transitive_closure.cpp:46:41: warning: '*((void*)(& ei)+16).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator >*, std::vector >, std::allocator > > > >, unsigned int, boost::detail::edge_desc_impl, int>::m_src' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(eList)[i++] = source(*ei, TC); ~~~~~~^~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c wavefront.cpp -o wavefront.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o RBGL.dll tmp.def bbc.o cliques.o clusteringCoef.o dominatorTree.o edmonds_optimum_branching.o hcs.o incrConnComp.o interfaces.o minST.o mincut.o ordering.o planar.o registerSigHandlers.o shortestPath.o sna.o transitive_closure.o wavefront.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/RBGL.buildbin-libdir/00LOCK-RBGL/00new/RBGL/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'RBGL' finding HTML links ... done FileDep html RBGL.overview html astarSearch html bandwidth html bccluster html bellman.ford.sp html betweenness html bfs html biConnComp html boyerMyrvoldPlanarityTest html chrobakPayneStraightLineDrawing html clusteringCoef html clusteringCoefAppr html coloring html connectedComp html dag.sp html defunct html dijkstra.sp html dominatorTree html edgeConn html edmondsMaxCardinalityMatching html edmondsOptimumBranching html extractPath html floyd.warshall.all.pairs.sp html gprofile html graphGenerator html highlyConnSG html incrConnComp html is.triangulated html isKuratowskiSubgraph html isStraightLineDrawing html isomorphism html johnson.all.pairs.sp html kCliques html kCores html lambdaSets html layout html makeBiconnectedPlanar html makeConnected html makeMaximalPlanar html maxClique html maxFlow html maximumCycleRatio html minCut html minimumCycleRatio html mstree.kruskal html mstree.prim html ordering html planarCanonicalOrdering html planarFaceTraversal html removeSelfLoops html separates html sloanStartEndVertices html sp.between html strongComp html transClosure html transitivity html tsort html wavefront html ** building package indices ** installing vignettes 'RBGL.Rnw' ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'RBGL' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bbc.cpp -o bbc.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from bbc.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cliques.cpp -o cliques.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from cliques.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c clusteringCoef.cpp -o clusteringCoef.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from clusteringCoef.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clusteringCoef.cpp: In function 'SEXPREC* graphGenerator(SEXP, SEXP, SEXP)': clusteringCoef.cpp:394:40: warning: 'u' may be used uninitialized in this function [-Wmaybe-uninitialized] Graph_ud::vertex_descriptor v, u, w=Graph_ud::null_vertex(); ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dominatorTree.cpp -o dominatorTree.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from dominatorTree.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from edmonds_optimum_branching.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from edmonds_optimum_branching.hpp:94, from edmonds_optimum_branching.cpp:3: edmonds_optimum_branching_impl.hpp: In function 'void edmonds_optimum_branching(TEdgeListGraph&, TVertexIndexMap, TWeightMap, TInputIterator, TInputIterator, TOutputIterator)': edmonds_optimum_branching_impl.hpp:520:71: warning: typedef 'EdgeIter' locally defined but not used [-Wunused-local-typedefs] typedef typename graph_traits::edge_iterator EdgeIter; ^~~~~~~~ edmonds_optimum_branching_impl.hpp:521:71: warning: typedef 'weight_t' locally defined but not used [-Wunused-local-typedefs] typedef typename property_traits::value_type weight_t; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hcs.cpp -o hcs.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from hcs.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from mincut.hpp:4, from hcs.cpp:2: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function 'typename boost::graph_traits::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = const R_adjacency_list; OutputIterator = std::back_insert_iterator >]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] typename Traits::vertex_descriptor p; ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c incrConnComp.cpp -o incrConnComp.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from incrConnComp.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from incrConnComp.cpp:2: incrConnComp.cpp: In function 'SEXPREC* BGL_incr_comp_internal(SEXP, SEXP, SEXP, E_IC_METHOD)': incrConnComp.cpp:74:32: warning: unused variable 'child_index' [-Wunused-variable] BOOST_FOREACH(VertexIndex child_index, components[current_index]) { ^~~~~~~~~~~ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:1114:14: note: in definition of macro 'BOOST_FOREACH' for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true) ^~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c interfaces.cpp -o interfaces.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from interfaces.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_tsort_D(SEXP, SEXP, SEXP)': interfaces.cpp:81:17: warning: catching polymorphic type 'struct boost::not_a_dag' by value [-Wcatch-value=] catch ( not_a_dag ) ^~~~~~~~~ interfaces.cpp:57:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^~~~ interfaces.cpp:61:62: warning: typedef 'Color' locally defined but not used [-Wunused-local-typedefs] typedef property_map::type Color; ^~~~~ interfaces.cpp: In function 'SEXPREC* BGL_bfs_D(SEXP, SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:98:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^~~~ interfaces.cpp:99:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; ^~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_dfs_D(SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:142:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^~~~ interfaces.cpp:143:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; ^~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_connected_components_U(SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:198:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::edge_descriptor Edge; ^~~~ interfaces.cpp:199:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; ^~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_strong_components_D(SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:225:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^~~~ interfaces.cpp:226:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; ^~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_biconnected_components_U(SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:252:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::edge_descriptor Edge; ^~~~ interfaces.cpp:253:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; ^~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_articulation_points_U(SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:295:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::edge_descriptor Edge; ^~~~ interfaces.cpp: In function 'SEXPREC* BGL_edge_connectivity_U(SEXP, SEXP, SEXP, SEXP)': interfaces.cpp:320:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; ^~~~~~ interfaces.cpp: In function 'SEXPREC* BGL_sequential_vertex_coloring(SEXP, SEXP, SEXP)': interfaces.cpp:360:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::edge_descriptor Edge; ^~~~ interfaces.cpp:361:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; ^~~~~~ In file included from interfaces.cpp:7: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function 'typename boost::graph_traits::degree_size_type boost::edge_connectivity(VertexListGraph&, OutputIterator) [with VertexListGraph = R_adjacency_list; OutputIterator = std::back_insert_iterator > >]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] typename Traits::vertex_descriptor p; ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c minST.cpp -o minST.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ minST.cpp: In function 'SEXPREC* BGL_KMST_D(SEXP, SEXP, SEXP, SEXP)': minST.cpp:14:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; ^~~~~~ minST.cpp: In function 'SEXPREC* BGL_KMST_U(SEXP, SEXP, SEXP, SEXP)': minST.cpp:48:62: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; ^~~~~~ minST.cpp: In function 'SEXPREC* BGL_PRIM_U(SEXP, SEXP, SEXP, SEXP)': minST.cpp:81:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_ud >::edge_descriptor Edge; ^~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'void boost::detail::kruskal_mst_impl(const Graph&, OutputIterator, Rank, Parent, Weight) [with Graph = R_adjacency_list; OutputIterator = std::back_insert_iterator > >; Rank = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, long long unsigned int>, long long unsigned int, long long unsigned int&>; Parent = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, long long unsigned int>, long long unsigned int, long long unsigned int&>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& ei +48)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from minST.cpp:2: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:55: note: '*((void*)& ei +48)' was declared here typename graph_traits< Graph >::edge_iterator ei, eiend; ^~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:32, from RBGL.hpp:38, from minST.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/edge.hpp:27:71: warning: '*((void*)& ei +40)' may be used uninitialized in this function [-Wmaybe-uninitialized] inline edge_base(Vertex s, Vertex d) : m_source(s), m_target(d) {} ^ In file included from minST.cpp:2: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:55: note: '*((void*)& ei +40)' was declared here typename graph_traits< Graph >::edge_iterator ei, eiend; ^~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mincut.cpp -o mincut.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'SEXPREC* BGL_max_flow_internal(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, E_MF_METHOD)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& ei +48)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ mincut.cpp:99:19: note: '*((void*)& ei +48)' was declared here edge_iterator ei, e_end; ^~ mincut.cpp:103:33: warning: '*((void*)& ei +40)' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(eList)[i++] = source(*ei, flow_g); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from mincut.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:148:48: warning: '*((void*)& ei +32)' may be used uninitialized in this function [-Wmaybe-uninitialized] &(*this->base()).get_property()); ^ mincut.cpp:99:19: note: '*((void*)& ei +32)' was declared here edge_iterator ei, e_end; ^~ In file included from mincut.hpp:4, from mincut.cpp:2: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function 'typename boost::graph_traits::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = R_adjacency_list; OutputIterator = std::back_insert_iterator >]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: 'p' may be used uninitialized in this function [-Wmaybe-uninitialized] typename Traits::vertex_descriptor p; ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ordering.cpp -o ordering.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from ordering.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/king_ordering.hpp:18, from ordering.cpp:9: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ordering.cpp: In function 'SEXPREC* BGL_min_degree_ordering(SEXP, SEXP, SEXP, SEXP)': ordering.cpp:133:53: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits::vertex_descriptor Vertex; ^~~~~~ ordering.cpp: In function 'SEXPREC* BGL_king_ordering(SEXP, SEXP, SEXP, SEXP)': ordering.cpp:182:48: warning: variable 'id' set but not used [-Wunused-but-set-variable] property_map::type id = get(vertex_index, g); ^~ ordering.cpp:176:53: warning: typedef 'Vertex' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits::vertex_descriptor Vertex; ^~~~~~ ordering.cpp: In function 'SEXPREC* BGL_sloan_ordering(SEXP, SEXP, SEXP, SEXP, SEXP)': ordering.cpp:232:47: warning: typedef 'Pair' locally defined but not used [-Wunused-local-typedefs] typedef std::pair Pair; ^~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c planar.cpp -o planar.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from planar.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ planar.cpp: In function 'SEXPREC* planarFaceTraversal(SEXP, SEXP, SEXP)': planar.cpp:161:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for ( int i = 0; i < v_vis.f_vis.size(); i++ ) ~~^~~~~~~~~~~~~~~~~~~~ planar.cpp:165:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for ( int j = 0; j < v_vis.f_vis[i].size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~~ planar.cpp: In function 'SEXPREC* planarCanonicalOrdering(SEXP, SEXP, SEXP)': planar.cpp:256:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for ( int i = 0; i < ordering.size(); i++ ) ~~^~~~~~~~~~~~~~~~~ planar.cpp:225:34: warning: variable 'oi_end' set but not used [-Wunused-but-set-variable] Vertex_Vec_t::iterator oi, oi_end = ordering.end(); ^~~~~~ planar.cpp: In function 'SEXPREC* isStraightLineDrawing(SEXP, SEXP, SEXP, SEXP)': planar.cpp:369:28: warning: comparison of integer expressions of different signedness: 'int' and 'boost::detail::adj_list_gen, boost::property >, boost::vecS, boost::vecS, boost::undirectedS, boost::property, boost::property, boost::no_property, boost::listS>::config::vertices_size_type' {aka 'long long unsigned int'} [-Wsign-compare] for ( int i = 0, j = 0; i < num_vertices(g); i++ ) ~~^~~~~~~~~~~~~~~~~ planar.cpp: In function 'SEXPREC* isKuratowskiSubgraph(SEXP, SEXP, SEXP)': planar.cpp:429:36: warning: variable 'ki_end' set but not used [-Wunused-but-set-variable] Edge_Vec_t::iterator ki, ki_end = kuratowski_edges.end(); ^~~~~~ planar.cpp:461:6: warning: unused variable 'i' [-Wunused-variable] int i, j = 0; ^ In file included from planar.cpp:6: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/chrobak_payne_drawing.hpp: In function 'void boost::chrobak_payne_straight_line_drawing(const Graph&, PlanarEmbedding, ForwardIterator, ForwardIterator, GridPositionMap, VertexIndexMap) [with Graph = boost::adjacency_list, boost::property >; PlanarEmbedding = boost::iterator_property_map<__gnu_cxx::__normal_iterator >*, std::vector > > >, boost::vec_adj_list_vertex_id_map, long long unsigned int> >; ForwardIterator = __gnu_cxx::__normal_iterator >; GridPositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator >, boost::vec_adj_list_vertex_id_map, long long unsigned int> >; VertexIndexMap = boost::vec_adj_list_vertex_id_map, long long unsigned int>]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/chrobak_payne_drawing.hpp:207:22: warning: 'next_to_rightmost' may be used uninitialized in this function [-Wmaybe-uninitialized] vertex_t next_to_rightmost; ^~~~~~~~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12, from planar.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp: In member function 'void boost::boyer_myrvold_impl::extract_kuratowski_subgraph(OutputIterator, EdgeIndexMap) [with OutputIterator = std::back_insert_iterator > >; EdgeIndexMap = boost::adj_list_edge_property_map, boost::edge_index_t>; Graph = boost::adjacency_list, boost::property >; VertexIndexMap = boost::vec_adj_list_vertex_id_map, long long unsigned int>; StoreOldHandlesPolicy = boost::graph::detail::store_old_handles; StoreEmbeddingPolicy = boost::graph::detail::no_embedding]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1264:9: warning: 'bicomp_root' may be used uninitialized in this function [-Wmaybe-uninitialized] if (bicomp_root != v) ^~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:19, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12, from planar.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/named_function_params.hpp: In static member function 'static bool boost::maximum_cardinality_matching_verifier::verify_matching(const Graph&, MateMap, VertexIndexMap) [with Graph = R_adjacency_list; MateMap = long long unsigned int*; VertexIndexMap = boost::vec_adj_list_vertex_id_map, long long unsigned int>]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:192:64: warning: '*((void*)& occ +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] bgl_named_params(T v, const Base& b) : m_value(v), m_base(b) {} ^ In file included from planar.cpp:11: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/max_cardinality_matching.hpp:778:52: note: '*((void*)& occ +16)' was declared here detail::odd_components_counter< v_size_t > occ(num_odd_components); ^~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c registerSigHandlers.cpp -o registerSigHandlers.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from registerSigHandlers.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c shortestPath.cpp -o shortestPath.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ shortestPath.cpp: In function 'SEXPREC* BGL_dijkstra_shortest_paths_D(SEXP, SEXP, SEXP, SEXP, SEXP)': shortestPath.cpp:17:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^~~~ shortestPath.cpp: In function 'SEXPREC* BGL_dag_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)': shortestPath.cpp:136:60: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef graph_traits < Graph_dd >::edge_descriptor Edge; ^~~~ shortestPath.cpp: In function 'SEXPREC* BGL_floyd_warshall_all_pairs_shortest_paths_D(SEXP, SEXP, SEXP, SEXP)': shortestPath.cpp:177:81: warning: typedef 'Graph' locally defined but not used [-Wunused-local-typedefs] property< edge_weight_t, double, property< edge_weight2_t, double > > > Graph; ^~~~~ shortestPath.cpp:180:39: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef std::pair < int, int >Edge; ^~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list, boost::property >, boost::no_property, boost::listS>; Size = long long unsigned int; WeightMap = boost::adj_list_edge_property_map >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& i +48)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28, from shortestPath.cpp:4: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: '*((void*)& i +48)' was declared here typename GTraits::edge_iterator i, end; ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list >; Size = int; WeightMap = boost::adj_list_edge_property_map, boost::edge_weight_t>; PredecessorMap = long long unsigned int*; DistanceMap = double*; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& i +48)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28, from shortestPath.cpp:4: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: '*((void*)& i +48)' was declared here typename GTraits::edge_iterator i, end; ^ In file included from RBGL.hpp:17, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:129:65: warning: '*((void*)& i +40)' may be used uninitialized in this function [-Wmaybe-uninitialized] inline const T& get(const T* pa, std::ptrdiff_t k) { return pa[k]; } ~~^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28, from shortestPath.cpp:4: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: '*((void*)& i +40)' was declared here typename GTraits::edge_iterator i, end; ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::floyd_warshall_all_pairs_shortest_paths(const VertexAndEdgeListGraph&, DistanceMatrix&, const WeightMap&, const BinaryPredicate&, const BinaryFunction&, const Infinity&, const Zero&) [with VertexAndEdgeListGraph = R_adjacency_list; DistanceMatrix = Basic2DMatrix; WeightMap = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; Zero = double]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& first +48)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from shortestPath.cpp:7: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:101:68: note: '*((void*)& first +48)' was declared here typename graph_traits< VertexAndEdgeListGraph >::edge_iterator first, last; ^~~~~ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:113:14: warning: '*((void*)& first +40)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (d[source(*first, g)][target(*first, g)] != inf) ~^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'SEXPREC* BGL_bellman_ford_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& ei +48)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ shortestPath.cpp:101:50: note: '*((void*)& ei +48)' was declared here graph_traits< EdgeGraph >::edge_iterator ei, ei_end; ^~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list; DistanceMatrix = Basic2DMatrix; VertexID = boost::vec_adj_list_vertex_id_map, long long unsigned int>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; DistanceZero = double]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& e +48)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from shortestPath.cpp:4: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: '*((void*)& e +48)' was declared here typename Traits2::edge_iterator e, e_end; ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_array.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/d_ary_heap.hpp:20, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/dijkstra_shortest_paths.hpp:20, from shortestPath.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_array.hpp:201:18: warning: '*((void*)& e +40)' may be used uninitialized in this function [-Wmaybe-uninitialized] return px[i]; ~~^ In file included from shortestPath.cpp:4: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: '*((void*)& e +40)' was declared here typename Traits2::edge_iterator e, e_end; ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: warning: '*((void*)(& e)+32).__gnu_cxx::__normal_iterator > >*, std::vector > >, std::allocator > > > > >::_M_current' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& e +48)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from shortestPath.cpp:4: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:84:41: note: '*((void*)& e +48)' was declared here typename Traits1::edge_iterator e, e_end; ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:89:41: warning: '*((void*)& e +40)' may be used uninitialized in this function [-Wmaybe-uninitialized] boost::tie(e2, z) = add_edge( ~~~~~~~~^ get(id1, source(*e, g1)) + 1, get(id1, target(*e, g1)) + 1, g2); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sna.cpp -o sna.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ sna.cpp: In function 'SEXPREC* lambdaSets(SEXP, SEXP, SEXP, SEXP)': sna.cpp:161:9: warning: variable 'res_cap' set but not used [-Wunused-but-set-variable] res_cap = get(edge_residual_capacity, flow_g); ^~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list, boost::property >, boost::no_property, boost::listS>; Size = long long unsigned int; WeightMap = boost::adj_list_edge_property_map >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus; BinaryPredicate = std::less; BellmanFordVisitor = boost::bellman_visitor<>]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& i +48)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28, from sna.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: '*((void*)& i +48)' was declared here typename GTraits::edge_iterator i, end; ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from sna.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list; DistanceMatrix = Basic2DMatrix; VertexID = boost::vec_adj_list_vertex_id_map, long long unsigned int>; Weight = boost::adj_list_edge_property_map, boost::edge_weight_t>; BinaryPredicate = std::less; BinaryFunction = boost::closed_plus; Infinity = double; DistanceZero = double]': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& e +48)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ In file included from sna.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: '*((void*)& e +48)' was declared here typename Traits2::edge_iterator e, e_end; ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/shared_array_property_map.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:27, from sna.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_array.hpp:201:18: warning: '*((void*)& e +40)' may be used uninitialized in this function [-Wmaybe-uninitialized] return px[i]; ~~^ In file included from sna.cpp:3: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: '*((void*)& e +40)' was declared here typename Traits2::edge_iterator e, e_end; ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c transitive_closure.cpp -o transitive_closure.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21, from transitive_closure.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'SEXPREC* BGL_transitive_closure_D(SEXP, SEXP, SEXP)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: '*((void*)& ei +48)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first ^~ transitive_closure.cpp:43:33: note: '*((void*)& ei +48)' was declared here Graph_dd::edge_iterator ei, e_end; ^~ transitive_closure.cpp:46:33: warning: '*((void*)& ei +40)' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(eList)[i++] = source(*ei, TC); ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c wavefront.cpp -o wavefront.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-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>&&)': C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from wavefront.cpp:1: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o RBGL.dll tmp.def bbc.o cliques.o clusteringCoef.o dominatorTree.o edmonds_optimum_branching.o hcs.o incrConnComp.o interfaces.o minST.o mincut.o ordering.o planar.o registerSigHandlers.o shortestPath.o sna.o transitive_closure.o wavefront.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/RBGL.buildbin-libdir/RBGL/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'RBGL' as RBGL_1.70.0.zip * DONE (RBGL) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'RBGL' successfully unpacked and MD5 sums checked