##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=CytoML.buildbin-libdir CytoML_2.7.2.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'CytoML' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
rm -f RcppExports.o parseFlowJoWorkspace.o CytoML.dll
"D:/biocbuild/bbs-3.15-bioc/R/bin/x64/Rscript.exe" "../tools/winlibs.R" 2.9.8
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function.hpp:30,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)':
../inst/include/CytoML/flowJoWorkspace.hpp:605:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for(int j = 0; j < sample_ids.size(); j++)
                  ~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
                 from parseFlowJoWorkspace.cpp:9:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function.hpp:30,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)':
../inst/include/CytoML/flowJoWorkspace.hpp:605:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for(int j = 0; j < sample_ids.size(); j++)
                  ~~^~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o CytoML.dll tmp.def RcppExports.o parseFlowJoWorkspace.o -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -L../windows/libxml2-2.9.8/lib/x64 -lxml2 -llzma -liconv -lz D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/lib/x64/libcytolib.a D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o -LD:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/lib/x64 -lprotobuf -LD:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LD:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CytoML'
    finding HTML links ... done
    CytoML-deprecated                       html  
    CytoML.par.get                          html  
    CytoML.par.init                         html  
    addCustomInfo                           html  
    ce_get_channels                         html  
    ce_get_compensations                    html  
    ce_get_markers                          html  
    ce_get_panels                           html  
    ce_get_samples                          html  
    ce_get_transformations                  html  
    compensate-GatingSet-graphGML-method    html  
    constructTree                           html  
    cytobank_experiment-methods             html  
    cytobank_to_gatingset                   html  
    diva_get_samples                        html  
    diva_to_gatingset                       html  
    diva_workspace-class                    html  
    finding level-2 HTML links ... done

    extend                                  html  
    fj_ws_get_keywords                      html  
    fj_ws_get_sample_groups                 html  
    fj_ws_get_samples                       html  
    flowjo_to_gatingset                     html  
    flowjo_workspace-class                  html  
    gatingset_to_cytobank                   html  
    gatingset_to_flowjo                     html  
    getChildren-graphGML-character-method   html  
    getCompensationMatrices.graphGML        html  
    getGate-graphGML-character-method       html  
    getNodes-graphGML-method                html  
    getParent-graphGML-character-method     html  
    getTransformations.graphGML             html  
    graphGML-class                          html  
    gs_compare_cytobank_counts              html  
    matchPath                               html  
    open_cytobank_experiment                html  
    open_diva_xml                           html  
    open_flowjo_xml                         html  
    parse.gateInfo                          html  
    plot-graphGML-missing-method            html  
    range.GatingHierarchy                   html  
    read.gatingML.cytobank                  html  
    show-graphGML-method                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'CytoML' as CytoML_2.7.2.zip
* DONE (CytoML)