##############################################################################
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###
### Running command:
###
###   rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_2.10.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CytoML.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CytoML.buildbin-libdir CytoML_2.10.0.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/MacOSX.sdk/usr/include -ftemplate-depth=900
configure:    PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX.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/MacOSX.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/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/flowWorkspace/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cpp11.cpp -o cpp11.o
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:5:
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:
../inst/include/CytoML/workspace_type.hpp:67:44: warning: 'recursive_directory_iterator' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
        for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
                                           ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/filesystem/directory.hpp:576:5: note: 'recursive_directory_iterator' has been explicitly marked deprecated here
    BOOST_FILESYSTEM_DETAIL_DEPRECATED("Use directory_options instead of symlink_option")
    ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/filesystem/config.hpp:85:64: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED'
#define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) __attribute__((deprecated(msg)))
                                                               ^
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:5:
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:
../inst/include/CytoML/workspace_type.hpp:67:44: warning: 'recursive_directory_iterator' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
        for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
                                           ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/filesystem/directory.hpp:576:5: note: 'recursive_directory_iterator' has been explicitly marked deprecated here
    BOOST_FILESYSTEM_DETAIL_DEPRECATED("Use directory_options instead of symlink_option")
    ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/filesystem/config.hpp:85:64: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED'
#define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) __attribute__((deprecated(msg)))
                                                               ^
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:5:
In file included from ../inst/include/CytoML/openWorkspace.hpp:12:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: 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/MacOSX.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/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/flowWorkspace/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from parseFlowJoWorkspace.cpp:10:
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:
../inst/include/CytoML/workspace_type.hpp:67:44: warning: 'recursive_directory_iterator' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
        for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
                                           ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/filesystem/directory.hpp:576:5: note: 'recursive_directory_iterator' has been explicitly marked deprecated here
    BOOST_FILESYSTEM_DETAIL_DEPRECATED("Use directory_options instead of symlink_option")
    ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/filesystem/config.hpp:85:64: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED'
#define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) __attribute__((deprecated(msg)))
                                                               ^
In file included from parseFlowJoWorkspace.cpp:10:
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:
../inst/include/CytoML/workspace_type.hpp:67:44: warning: 'recursive_directory_iterator' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
        for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
                                           ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/filesystem/directory.hpp:576:5: note: 'recursive_directory_iterator' has been explicitly marked deprecated here
    BOOST_FILESYSTEM_DETAIL_DEPRECATED("Use directory_options instead of symlink_option")
    ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include/boost/filesystem/config.hpp:85:64: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED'
#define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) __attribute__((deprecated(msg)))
                                                               ^
In file included from parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/CytoML/openWorkspace.hpp:12:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: 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 cpp11.o parseFlowJoWorkspace.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 -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.16-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/4.2/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/4.2/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/4.2/Resources/lib/libquadmath.0.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"