##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowWorkspace_4.8.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R flowWorkspace.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowWorkspace.buildbin-libdir flowWorkspace_4.8.0.tar.gz'
>>>>>>> 

* 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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_API.cpp -o R_API.o
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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_GatingSet.cpp -o R_GatingSet.o
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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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:6:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:46:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/Rcpp/include/Rcpp/XPtr.h:54:26: 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++ -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cytoctxAPI.cpp -o cytoctxAPI.o
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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:46:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/Rcpp/include/Rcpp/XPtr.h:54:26: 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++ -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:46:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/Rcpp/include/Rcpp/XPtr.h:54:26: 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++ -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getDescendants.cpp -o getDescendants.o
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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getPopStats.cpp -o getPopStats.o
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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getSingleCellExpression.cpp -o getSingleCellExpression.o
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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c h5_error_r_handler.cpp -o h5_error_r_handler.o
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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c setCounts.cpp -o setCounts.o
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 cytoctxAPI.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o /Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib -lsz -laec -lz -ldl -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.15-bioc/meat/flowWorkspace.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING LINKS FOR flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so"