############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoML.buildbin-libdir CytoML_2.4.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * 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 "C:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386/Rscript.exe" "../tools/winlibs.R" 2.9.8 "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use instead. BOOST_HEADER_DEPRECATED("") ^ 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::flowJoWorkspace::get_sample_info(const std::vector >&, const CytoML::ParseWorkspaceParameters&)': ../inst/include/CytoML/flowJoWorkspace.hpp:598:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int j = 0; j < sample_ids.size(); j++) ~~^~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use instead. BOOST_HEADER_DEPRECATED("") ^ 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::flowJoWorkspace::get_sample_info(const std::vector >&, const CytoML::ParseWorkspaceParameters&)': ../inst/include/CytoML/flowJoWorkspace.hpp:598:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int j = 0; j < sample_ids.size(); j++) ~~^~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o CytoML.dll tmp.def RcppExports.o parseFlowJoWorkspace.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -L../windows/libxml2-2.9.8/lib/i386 -lxml2 -llzma -liconv -lz C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/lib/i386/libcytolib.a C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/i386 -lprotobuf -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -lws2_32 -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/libs/i386 ** 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 install for x64 * installing *source* package 'CytoML' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs rm -f RcppExports.o parseFlowJoWorkspace.o CytoML.dll "C:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64/Rscript.exe" "../tools/winlibs.R" 2.9.8 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use instead. BOOST_HEADER_DEPRECATED("") ^ 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::flowJoWorkspace::get_sample_info(const std::vector >&, const CytoML::ParseWorkspaceParameters&)': ../inst/include/CytoML/flowJoWorkspace.hpp:598:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int j = 0; j < sample_ids.size(); j++) ~~^~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from C:/Users/biocbuild/bbs-3.13-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 class auto_ptr; ^~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from C:/Users/biocbuild/bbs-3.13-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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use instead. BOOST_HEADER_DEPRECATED("") ^ 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::flowJoWorkspace::get_sample_info(const std::vector >&, const CytoML::ParseWorkspaceParameters&)': ../inst/include/CytoML/flowJoWorkspace.hpp:598:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int j = 0; j < sample_ids.size(); j++) ~~^~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o CytoML.dll tmp.def RcppExports.o parseFlowJoWorkspace.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -L../windows/libxml2-2.9.8/lib/x64 -lxml2 -llzma -liconv -lz C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/lib/x64/libcytolib.a C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/x64 -lprotobuf -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/Users/BIOCBU~1/BBS-3~1.13-/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 -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CytoML.buildbin-libdir/CytoML/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'CytoML' as CytoML_2.4.0.zip * DONE (CytoML)