##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> 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++ -arch arm64 -std=gnu++11 accepts -g... yes
checking for gcc... clang -arch arm64
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 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++ -arch arm64 -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-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/flowWorkspace/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c cpp11.cpp -o cpp11.o
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/flowWorkspace/include/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/transformation.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/split.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/iter_find.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/find_iterator.hpp:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function/detail/prologue.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/throw_exception.hpp:24:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/assert/source_location.hpp:75:14: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
        std::sprintf( buffer, ":%ld", static_cast<long>( line() ) );
             ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/flowWorkspace/include/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/transformation.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/split.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/iter_find.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/find_iterator.hpp:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function/detail/prologue.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/throw_exception.hpp:24:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/assert/source_location.hpp:80:18: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
            std::sprintf( buffer, ":%ld", static_cast<long>( column() ) );
                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/flowWorkspace/include/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
                    sprintf(begin,
                    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/flowWorkspace/include/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
                    sprintf(begin,
                    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/flowWorkspace/include/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
                    sprintf(begin,
                    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_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
                                    ^
6 warnings generated.
clang++ -arch arm64 -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-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/flowWorkspace/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -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:
In file included from ../inst/include/CytoML/workspace_type.hpp:4:
In file included from ../inst/include/CytoML/wsNode.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/transformation.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/split.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/iter_find.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/find_iterator.hpp:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function/detail/prologue.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/throw_exception.hpp:24:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/assert/source_location.hpp:75:14: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
        std::sprintf( buffer, ":%ld", static_cast<long>( line() ) );
             ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_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:
In file included from ../inst/include/CytoML/workspace_type.hpp:4:
In file included from ../inst/include/CytoML/wsNode.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/transformation.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/split.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/iter_find.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/find_iterator.hpp:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function/detail/prologue.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/throw_exception.hpp:24:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/assert/source_location.hpp:80:18: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
            std::sprintf( buffer, ":%ld", static_cast<long>( column() ) );
                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_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:
In file included from ../inst/include/CytoML/workspace_type.hpp:4:
In file included from ../inst/include/CytoML/wsNode.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
                    sprintf(begin,
                    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_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:
In file included from ../inst/include/CytoML/workspace_type.hpp:4:
In file included from ../inst/include/CytoML/wsNode.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
                    sprintf(begin,
                    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_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:
In file included from ../inst/include/CytoML/workspace_type.hpp:4:
In file included from ../inst/include/CytoML/wsNode.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
                    sprintf(begin,
                    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_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
                                    ^
6 warnings generated.
clang++ -arch arm64 -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/opt/R/arm64/lib -o CytoML.so cpp11.o parseFlowJoWorkspace.o /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.2-arm64/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
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/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 "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"