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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL flowWorkspace
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
make: R: Command not found
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_API.cpp -o R_API.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_GatingSet.cpp -o R_GatingSet.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:46:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:34,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from ../inst/include/flowWorkspace.h:6,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of ‘void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]’:
RcppExports.cpp:593:52:   required from here
/home/biocbuild/bbs-3.11-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;
     ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:46:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:34,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from cytoframeAPI.cpp:2:
/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of ‘void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]’:
cytoframeAPI.cpp:8:52:   required from here
/home/biocbuild/bbs-3.11-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;
     ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cytosetAPI.cpp -o cytosetAPI.o
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:46:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:34,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from cytosetAPI.cpp:2:
/home/biocbuild/bbs-3.11-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
/home/biocbuild/bbs-3.11-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;
     ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getDescendants.cpp -o getDescendants.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getPopStats.cpp -o getPopStats.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getSingleCellExpression.cpp -o getSingleCellExpression.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5_error_r_handler.cpp -o h5_error_r_handler.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c setCounts.cpp -o setCounts.o
mkdir -p "/home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib"
ar rs "/home/biocbuild/bbs-3.11-bioc/R/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 /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/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/home/biocbuild/bbs-3.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
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 /home/biocbuild/bbs-3.11-bioc/R/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)