############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/flowWorkspace_4.4.0.tar.gz && rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowWorkspace.buildbin-libdir flowWorkspace_4.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_4.4.0.zip && rm flowWorkspace_4.4.0.tar.gz flowWorkspace_4.4.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 11 4651k 11 537k 0 0 1188k 0 0:00:03 --:--:-- 0:00:03 1190k 72 4651k 72 3351k 0 0 2255k 0 0:00:02 0:00:01 0:00:01 2255k 100 4651k 100 4651k 0 0 2501k 0 0:00:01 0:00:01 --:--:-- 2500k install for i386 * installing *source* package 'flowWorkspace' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_API.cpp -o R_API.o 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 R_API.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/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 R_API.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/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 R_API.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("") ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o 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 R_GatingHierarchy.cpp:17: 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/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 R_GatingHierarchy.cpp:17: 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/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 R_GatingHierarchy.cpp:17: 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("") ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_GatingSet.cpp -o R_GatingSet.o 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 ../inst/include/flowWorkspace.h:5, from R_GatingSet.cpp:10: 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/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 ../inst/include/flowWorkspace.h:5, from R_GatingSet.cpp:10: 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/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/flowWorkspace.h:5, from R_GatingSet.cpp:10: 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("") ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o 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 ../inst/include/flowWorkspace.h:5, 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/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 ../inst/include/flowWorkspace.h:5, 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/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/flowWorkspace.h:5, 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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32, from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15, from ../inst/include/flowWorkspace.h:6, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]': RcppExports.cpp:629:43: required from here C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete obj; ^~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cytoctxAPI.cpp -o cytoctxAPI.o 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 ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12, from cytoctxAPI.cpp:1: 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/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 ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12, from cytoctxAPI.cpp:1: 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/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/flowWorkspace/pairVectorRcppWrap.h:12, from cytoctxAPI.cpp:1: 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("") ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cytoframeAPI.cpp -o cytoframeAPI.o 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/H5CytoFrame.hpp:12, from cytoframeAPI.cpp:1: 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/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/H5CytoFrame.hpp:12, from cytoframeAPI.cpp:1: 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/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/flowWorkspace/pairVectorRcppWrap.h:12, from cytoframeAPI.cpp:3: 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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32, from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15, from cytoframeAPI.cpp:3: C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]': cytoframeAPI.cpp:9:43: required from here C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete obj; ^~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cytosetAPI.cpp -o cytosetAPI.o 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/H5CytoFrame.hpp:12, from cytosetAPI.cpp:1: 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/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/H5CytoFrame.hpp:12, from cytosetAPI.cpp:1: 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/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/flowWorkspace/pairVectorRcppWrap.h:12, from cytosetAPI.cpp:2: 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("") ^ cytosetAPI.cpp: In function 'Rcpp::XPtr get_cytoframe(Rcpp::XPtr, Rcpp::RObject, Rcpp::RObject)': cytosetAPI.cpp:206:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for(unsigned i = 0; i < j_val.size(); i++){ ~~^~~~~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32, from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15, from cytosetAPI.cpp:2: C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]': cytosetAPI.cpp:38:81: required from here C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete obj; ^~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getDescendants.cpp -o getDescendants.o 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 getDescendants.cpp:1: 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/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 getDescendants.cpp:1: 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/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 getDescendants.cpp:1: 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("") ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getPopStats.cpp -o getPopStats.o 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 getPopStats.cpp:1: 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/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 getPopStats.cpp:1: 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/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 getPopStats.cpp:1: 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("") ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getSingleCellExpression.cpp -o getSingleCellExpression.o 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 getSingleCellExpression.cpp:1: 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/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 getSingleCellExpression.cpp:1: 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/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 getSingleCellExpression.cpp:1: 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("") ^ getSingleCellExpression.cpp: In function 'Rcpp::NumericMatrix getSingleCellExpressionByGate(Rcpp::XPtr, std::__cxx11::string, Rcpp::List, Rcpp::NumericMatrix, Rcpp::CharacterVector, bool)': getSingleCellExpression.cpp:74:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for(unsigned j = 0; j < pops.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 -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5_error_r_handler.cpp -o h5_error_r_handler.o 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 ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12, from h5_error_r_handler.cpp:8: 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/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 ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12, from h5_error_r_handler.cpp:8: 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/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/flowWorkspace/pairVectorRcppWrap.h:12, from h5_error_r_handler.cpp:8: 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("") ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c setCounts.cpp -o setCounts.o 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 setCounts.cpp:1: 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/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 setCounts.cpp:1: 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/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 setCounts.cpp:1: 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("") ^ mkdir -p "C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386" "C:/rtools40/mingw32/bin/"ar rs "C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoctxAPI.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o C:\rtools40\mingw32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386/libflowWorkspace.a C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoctxAPI.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.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 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/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'flowWorkspace' finding HTML links ... done GatingHierarchy-class html GatingSet-class html GatingSet-methods html GatingSetList-class html asinh_Gml2 html asinhtGml2_trans html booleanFilter-class html finding level-2 HTML links ... done brackets html cf_append_cols html cf_backend_type html cf_get_uri html cf_write_disk html cf_write_h5 html cf_write_tile html cleanup html cleanup_temp html compensate html convert html convert_backend html convert_legacy html cs_add_cytoframe html cs_get_uri html cs_set_cytoframe html cytoctx html cytoframe-labels html cytoframe html cytoset html default_backend html delete_gs html estimateLogicle html extract_cluster_pop_name_from_node html filter_to_list html flowWorkspace-deprecated html flowWorkspace-package html flow_breaks html flow_trans html flowjo_biexp html flowjo_biexp_trans html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/help/flowJo_biexp_trans.html flowjo_fasinh html flowjo_fasinh_trans html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/help/flowJo_fasinh_trans.html flowjo_log_trans html gh_apply_to_cs html gh_apply_to_new_fcs html gh_copy_gate html gh_get_cluster_labels html gh_get_compensations html gh_get_transformations html gh_pop_compare_stats html gh_pop_get_cluster_name html gh_pop_get_data html gh_pop_get_descendants html gh_pop_get_full_path html gh_pop_get_indices html gh_pop_get_indices_mat html gh_pop_get_proportion html gh_pop_move html gh_pop_set_indices html gh_pop_set_xml_count html gs_check_redundant_nodes html gs_cyto_data html gs_get_compensation_internal html gs_get_leaf_nodes html gs_get_pop_paths html gs_get_singlecell_expression html gs_is_persistent html gs_plot_diff_tree html gs_plot_pop_count_cv html gs_pop_add html gs_pop_get_children html gs_pop_get_count_fast html gs_pop_get_gate html gs_pop_get_gs html gs_pop_get_stats html gs_pop_get_stats_tfilter html gs_pop_set_gate html gs_pop_set_name html gs_pop_set_visibility html gs_remove_redundant_channels html gs_remove_redundant_nodes html gs_split_by_channels html gs_split_by_tree html gs_update_channels html gslist_to_gs html identifier-methods html is_subsetted html is_tiledb_support html keyword-mutators html keyword html lapply-methods html length html load_cytoframe html load_cytoframe_from_fcs html load_cytoset_from_fcs html load_meta html lock html logicleGml2_trans html logicle_trans html loglevel html logtGml2_trans html markernames html merge_list_to_gs html ncFlowSet-methods html nodeflags html openWorkspace html pData-methods html plot-methods html plotGate-methods-defunct html pop_add html prettyAxis html recompute html rotate_gate html sampleNames html save_cytoset html save_gs html scale_gate html shift_gate html standardize-GatingSet html stats.fun html subset html swap_data_cols html transform html transform_gate html transformerList 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 'flowWorkspace' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_API.cpp -o R_API.o 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 R_API.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/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 R_API.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/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 R_API.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("") ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o 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 R_GatingHierarchy.cpp:17: 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/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 R_GatingHierarchy.cpp:17: 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/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 R_GatingHierarchy.cpp:17: 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("") ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_GatingSet.cpp -o R_GatingSet.o 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 ../inst/include/flowWorkspace.h:5, from R_GatingSet.cpp:10: 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/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 ../inst/include/flowWorkspace.h:5, from R_GatingSet.cpp:10: 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/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/flowWorkspace.h:5, from R_GatingSet.cpp:10: 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("") ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o 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 ../inst/include/flowWorkspace.h:5, 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/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 ../inst/include/flowWorkspace.h:5, 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/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/flowWorkspace.h:5, 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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32, from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15, from ../inst/include/flowWorkspace.h:6, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]': RcppExports.cpp:629:43: required from here C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete obj; ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cytoctxAPI.cpp -o cytoctxAPI.o 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 ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12, from cytoctxAPI.cpp:1: 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/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 ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12, from cytoctxAPI.cpp:1: 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/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/flowWorkspace/pairVectorRcppWrap.h:12, from cytoctxAPI.cpp:1: 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("") ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cytoframeAPI.cpp -o cytoframeAPI.o 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/H5CytoFrame.hpp:12, from cytoframeAPI.cpp:1: 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/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/H5CytoFrame.hpp:12, from cytoframeAPI.cpp:1: 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/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/flowWorkspace/pairVectorRcppWrap.h:12, from cytoframeAPI.cpp:3: 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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32, from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15, from cytoframeAPI.cpp:3: C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]': cytoframeAPI.cpp:9:43: required from here C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete obj; ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cytosetAPI.cpp -o cytosetAPI.o 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/H5CytoFrame.hpp:12, from cytosetAPI.cpp:1: 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/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/H5CytoFrame.hpp:12, from cytosetAPI.cpp:1: 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/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/flowWorkspace/pairVectorRcppWrap.h:12, from cytosetAPI.cpp:2: 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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32, from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15, from cytosetAPI.cpp:2: C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]': cytosetAPI.cpp:38:81: required from here C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete obj; ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getDescendants.cpp -o getDescendants.o 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 getDescendants.cpp:1: 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/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 getDescendants.cpp:1: 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/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 getDescendants.cpp:1: 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("") ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getPopStats.cpp -o getPopStats.o 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 getPopStats.cpp:1: 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/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 getPopStats.cpp:1: 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/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 getPopStats.cpp:1: 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("") ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getSingleCellExpression.cpp -o getSingleCellExpression.o 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 getSingleCellExpression.cpp:1: 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/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 getSingleCellExpression.cpp:1: 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/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 getSingleCellExpression.cpp:1: 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("") ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5_error_r_handler.cpp -o h5_error_r_handler.o 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 ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12, from h5_error_r_handler.cpp:8: 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/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 ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12, from h5_error_r_handler.cpp:8: 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/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/flowWorkspace/pairVectorRcppWrap.h:12, from h5_error_r_handler.cpp:8: 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("") ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c setCounts.cpp -o setCounts.o 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 setCounts.cpp:1: 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/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 setCounts.cpp:1: 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/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 setCounts.cpp:1: 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("") ^ mkdir -p "C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64" "C:/rtools40/mingw64/bin/"ar rs "C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoctxAPI.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o C:\rtools40\mingw64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoctxAPI.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.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 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/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'flowWorkspace' as flowWorkspace_4.4.0.zip * DONE (flowWorkspace) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'flowWorkspace' successfully unpacked and MD5 sums checked