############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CytoML ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library' * 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 "F:/biocbuild/bbs-3.15-bioc/R/bin/x64/Rscript.exe" "../tools/winlibs.R" 2.9.10 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.10/include/libxml2 -DLIBXML_STATIC -fpermissive -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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] 435 | * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate | In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function.hpp:30, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 48 | template T * get_pointer(std::auto_ptr const& p) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) | ~~^~~~~~~~~~~~~~~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: F:/biocbuild/bbs-3.15-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>&&)': F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from ../inst/include/CytoML.h:5, from RcppExports.cpp:4: ../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector CytoML::flowJoWorkspace::get_sample_info(const std::vector >&, const CytoML::ParseWorkspaceParameters&)': ../inst/include/CytoML/flowJoWorkspace.hpp:605:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 605 | for(int j = 0; j < sample_ids.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.10/include/libxml2 -DLIBXML_STATIC -fpermissive -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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] 435 | * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate | In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from ../inst/include/CytoML/wsNode.hpp:13, from ../inst/include/CytoML/workspace_type.hpp:4, from ../inst/include/CytoML/workspace.hpp:10, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^ F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function.hpp:30, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from ../inst/include/CytoML/wsNode.hpp:13, from ../inst/include/CytoML/workspace_type.hpp:4, from ../inst/include/CytoML/workspace.hpp:10, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 48 | template T * get_pointer(std::auto_ptr const& p) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from ../inst/include/CytoML/wsNode.hpp:13, from ../inst/include/CytoML/workspace_type.hpp:4, from ../inst/include/CytoML/workspace.hpp:10, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from ../inst/include/CytoML/wsNode.hpp:13, from ../inst/include/CytoML/workspace_type.hpp:4, from ../inst/include/CytoML/workspace.hpp:10, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) | ~~^~~~~~~~~~~~~~~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from ../inst/include/CytoML/workspace.hpp:14, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from ../inst/include/CytoML/wsNode.hpp:13, from ../inst/include/CytoML/workspace_type.hpp:4, from ../inst/include/CytoML/workspace.hpp:10, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from ../inst/include/CytoML/workspace.hpp:14, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from ../inst/include/CytoML/wsNode.hpp:13, from ../inst/include/CytoML/workspace_type.hpp:4, from ../inst/include/CytoML/workspace.hpp:10, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from ../inst/include/CytoML/workspace.hpp:14, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from ../inst/include/CytoML/wsNode.hpp:13, from ../inst/include/CytoML/workspace_type.hpp:4, from ../inst/include/CytoML/workspace.hpp:10, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from ../inst/include/CytoML/workspace.hpp:14, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from ../inst/include/CytoML/wsNode.hpp:13, from ../inst/include/CytoML/workspace_type.hpp:4, from ../inst/include/CytoML/workspace.hpp:10, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from ../inst/include/CytoML/workspace.hpp:14, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from ../inst/include/CytoML/wsNode.hpp:13, from ../inst/include/CytoML/workspace_type.hpp:4, from ../inst/include/CytoML/workspace.hpp:10, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from ../inst/include/CytoML/workspace.hpp:14, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from ../inst/include/CytoML/wsNode.hpp:13, from ../inst/include/CytoML/workspace_type.hpp:4, from ../inst/include/CytoML/workspace.hpp:10, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from ../inst/include/CytoML/workspace.hpp:14, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from ../inst/include/CytoML/wsNode.hpp:13, from ../inst/include/CytoML/workspace_type.hpp:4, from ../inst/include/CytoML/workspace.hpp:10, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606, from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from ../inst/include/CytoML/workspace.hpp:14, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: F:/biocbuild/bbs-3.15-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>&&)': F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135, from F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from ../inst/include/CytoML/wsNode.hpp:13, from ../inst/include/CytoML/workspace_type.hpp:4, from ../inst/include/CytoML/workspace.hpp:10, from ../inst/include/CytoML/flowJoWorkspace.hpp:11, from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:9: ../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector CytoML::flowJoWorkspace::get_sample_info(const std::vector >&, const CytoML::ParseWorkspaceParameters&)': ../inst/include/CytoML/flowJoWorkspace.hpp:605:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 605 | for(int j = 0; j < sample_ids.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~ g++ -shared -s -static-libgcc -o CytoML.dll tmp.def RcppExports.o parseFlowJoWorkspace.o -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -L../windows/libxml2-2.9.10/lib/x64-ucrt -lxml2 -llzma -liconv -lz F:/biocbuild/bbs-3.15-bioc/R/library/cytolib/lib/x64/libcytolib.a F:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o -LF:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/lib/x64 -lprotobuf -LF:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LF:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -lws2_32 -lbcrypt -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-CytoML/00new/CytoML/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CytoML)