Multiple platform build/check report for BioC 3.9 - INSTALL report for flowWorkspace on malbec2

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL flowWorkspace
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_API.cpp -o R_API.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template T * get_pointer(std::auto_ptr const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template T * get_pointer(std::auto_ptr const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_GatingSet.cpp -o R_GatingSet.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template T * get_pointer(std::auto_ptr const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template T * get_pointer(std::auto_ptr const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c getDescendants.cpp -o getDescendants.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template T * get_pointer(std::auto_ptr const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c getPopStats.cpp -o getPopStats.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template T * get_pointer(std::auto_ptr const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template T * get_pointer(std::auto_ptr const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c setCounts.cpp -o setCounts.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template T * get_pointer(std::auto_ptr const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
mkdir -p "/home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib"
ar rs "/home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o
ar: creating /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o /home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/lib/GatingSet.pb.o /home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/lib/libprotobuf.a -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowWorkspace.so; fi
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowWorkspace)
INSTALL report for flowWorkspace on malbec2

Summary

Command output
