Package: flowWorkspace

Version: 3.35.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowWorkspace

StartedAt: 2020-01-15 18:42:25 -0500 (Wed, 15 Jan 2020)

EndedAt: 2020-01-15 18:46:47 -0500 (Wed, 15 Jan 2020)

EllapsedTime: 261.6 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowWorkspace
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment  -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_API.cpp -o R_API.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment  -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment  -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_GatingSet.cpp -o R_GatingSet.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment  -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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: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:31:5: 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:46:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<cytolib::CytoFrameView>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment  -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from cytoframeAPI.cpp:1:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/H5CytoFrame.hpp:47:7: warning: 'cytolib::H5CytoFrame::set_params' hides overloaded virtual function [-Woverloaded-virtual]
        void set_params(const vector<cytoParam> & _params)
             ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:115:15: note: hidden overloaded virtual function 'cytolib::CytoFrame::set_params' declared here: different number of parameters (2 vs 1)
        virtual void set_params(const vector<cytoParam> & _params, bool force = false);
                     ^
In file included from cytoframeAPI.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:31:5: 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:46:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<cytolib::CytoFrameView>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment  -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c cytosetAPI.cpp -o cytosetAPI.o
In file included from cytosetAPI.cpp:1:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/H5CytoFrame.hpp:47:7: warning: 'cytolib::H5CytoFrame::set_params' hides overloaded virtual function [-Woverloaded-virtual]
        void set_params(const vector<cytoParam> & _params)
             ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:115:15: note: hidden overloaded virtual function 'cytolib::CytoFrame::set_params' declared here: different number of parameters (2 vs 1)
        virtual void set_params(const vector<cytoParam> & _params, bool force = false);
                     ^
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:31:5: 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:46:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<cytolib::CytoFrameView>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment  -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c getDescendants.cpp -o getDescendants.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment  -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c getPopStats.cpp -o getPopStats.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment  -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c getSingleCellExpression.cpp -o getSingleCellExpression.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment  -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c h5_error_r_handler.cpp -o h5_error_r_handler.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment  -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' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c setCounts.cpp -o setCounts.o
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++ -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-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -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)