##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowWorkspace
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_API.cpp -o R_API.o
In file included from R_API.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:108:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from R_API.cpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from R_GatingHierarchy.cpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:108:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from R_GatingHierarchy.cpp:23:
In file included from ../inst/include/flowWorkspace/convert_trans.h:8:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_GatingSet.cpp -o R_GatingSet.o
In file included from R_GatingSet.cpp:10:
In file included from ../inst/include/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:108:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from R_GatingSet.cpp:10:
In file included from ../inst/include/flowWorkspace.h:6:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:108:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/flowWorkspace.h:6:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/flowWorkspace.h:6:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:46:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete obj;
    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/XPtr.h:53:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<cytolib::CytoFrameView>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from cytoframeAPI.cpp:3:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:116:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from cytoframeAPI.cpp:3:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
In file included from cytoframeAPI.cpp:3:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:46:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete obj;
    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/XPtr.h:53:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<cytolib::CytoFrameView>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cytosetAPI.cpp -o cytosetAPI.o
In file included from cytosetAPI.cpp:2:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:116:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from cytosetAPI.cpp:2:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
In file included from cytosetAPI.cpp:2:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:46:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete obj;
    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/XPtr.h:53:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<cytolib::CytoFrameView>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getDescendants.cpp -o getDescendants.o
In file included from getDescendants.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:108:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from getDescendants.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getPopStats.cpp -o getPopStats.o
In file included from getPopStats.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:108:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from getPopStats.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from getSingleCellExpression.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:108:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from getSingleCellExpression.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c h5_error_r_handler.cpp -o h5_error_r_handler.o
In file included from h5_error_r_handler.cpp:8:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:103:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from h5_error_r_handler.cpp:8:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c setCounts.cpp -o setCounts.o
In file included from setCounts.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:108:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from setCounts.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
2 warnings generated.
mkdir -p "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib"
ar rs "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o
ar: creating archive /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowWorkspace.so; fi
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-flowWorkspace/00new/flowWorkspace/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowWorkspace)