Multiple platform build/check report for BioC 3.6 - INSTALL report for cytolib on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD INSTALL cytolib
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* installing to library ‘/home/biocbuild/bbs-3.6-bioc/R/library’
* installing *source* package ‘cytolib’ ...
** libs
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c GatingSet.cpp -o GatingSet.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c GatingSet.pb.cc -o GatingSet.pb.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c POPINDICES.cpp -o POPINDICES.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c calibrationTable.cpp -o calibrationTable.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c compensation.cpp -o compensation.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/transformation.hpp:24,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c delimitedMessage.cpp -o delimitedMessage.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c ellipse2points.cpp -o ellipse2points.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c flowData.cpp -o flowData.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c gate.cpp -o gate.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c global.cpp -o global.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c nodeProperties.cpp -o nodeProperties.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c spline.cpp -o spline.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c transformation.cpp -o transformation.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/transformation.hpp:24,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
mkdir -p "/home/biocbuild/bbs-3.6-bioc/R/library/cytolib/lib"
ar rs "/home/biocbuild/bbs-3.6-bioc/R/library/cytolib/lib/libcytolib.a" GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o calibrationTable.o compensation.o delimitedMessage.o ellipse2points.o flowData.o gate.o global.o nodeProperties.o spline.o transformation.o
ar: creating /home/biocbuild/bbs-3.6-bioc/R/library/cytolib/lib/libcytolib.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o cytolib.so GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o calibrationTable.o compensation.o delimitedMessage.o ellipse2points.o flowData.o gate.o global.o nodeProperties.o spline.o transformation.o /home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/lib/libprotobuf.a -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/R/library/cytolib/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cytolib)
INSTALL report for cytolib on malbec1

Summary

Command output
