##############################################################################
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###
### Running command:
###
###   rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_2.2.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CytoML.buildbin-libdir
###
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##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CytoML.buildbin-libdir CytoML_2.2.2.tar.gz'
>>>>>>> 

* installing *source* package ‘CytoML’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++11 accepts -g... yes
checking for gcc... clang -mmacosx-version-min=10.13
checking whether we are using the GNU C compiler... yes
checking whether clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: setting cytolib-ml commandline tool path...
configure: Using the following compilation and linking flags
configure:    PKG_CPPFLAGS=-I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/libxml2 -ftemplate-depth=900
configure:    PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm 
configure:    CYTOLIBML_BIN=/usr/local/bin
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/cytolibml_bin_path.R
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/libxml2 -ftemplate-depth=900 -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'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowWorkspace/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/CytoML.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowWorkspace/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/CytoML.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowWorkspace/include/flowWorkspace.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowWorkspace/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/CytoML.h:5:
In file included from ../inst/include/CytoML/openWorkspace.hpp:12:
../inst/include/CytoML/winFlowJoWorkspace.hpp:439:30: warning: '/*' within block comment [-Wcomment]
           * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                                    ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/libxml2 -ftemplate-depth=900 -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'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowWorkspace/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from parseFlowJoWorkspace.cpp:9:
In file included from ../inst/include/CytoML/openWorkspace.hpp:11:
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11:
In file included from ../inst/include/CytoML/workspace.hpp:10:
In file included from ../inst/include/CytoML/workspace_type.hpp:4:
In file included from ../inst/include/CytoML/wsNode.hpp:17:
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 parseFlowJoWorkspace.cpp:9:
In file included from ../inst/include/CytoML/openWorkspace.hpp:11:
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11:
In file included from ../inst/include/CytoML/workspace.hpp:14:
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>:12:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from parseFlowJoWorkspace.cpp:9:
In file included from ../inst/include/CytoML/openWorkspace.hpp:12:
../inst/include/CytoML/winFlowJoWorkspace.hpp:439:30: warning: '/*' within block comment [-Wcomment]
           * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                                    ^
3 warnings generated.
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 CytoML.so RcppExports.o parseFlowJoWorkspace.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 -L/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib -lxml2 -lz -lpthread -licucore -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
installing to /Users/biocbuild/bbs-3.12-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/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 (CytoML)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"