##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowCore_2.10.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R flowCore.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowCore.buildbin-libdir flowCore_2.10.0.tar.gz'
>>>>>>> 

* installing *source* package ‘flowCore’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c FastLogicle.cpp -o FastLogicle.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c Hyperlog.cpp -o Hyperlog.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c Logicle.cpp -o Logicle.o
Logicle.cpp:46:2: 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(buffer, "Illegal argument value %.17g", value);
        ^
/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)))
                                                      ^
Logicle.cpp:52:2: 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(buffer, "Illegal argument value %d", value);
        ^
/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)))
                                                      ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c biexponential.cpp -o biexponential.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c convertRawBytes.cpp -o convertRawBytes.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c cpp11.cpp -o cpp11.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c fcsTextParse.cpp -o fcsTextParse.o
In file included from fcsTextParse.cpp:9:
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 fcsTextParse.cpp:9:
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 fcsTextParse.cpp:10:
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 fcsTextParse.cpp:10:
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 fcsTextParse.cpp:10:
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)))
                                                      ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c hyperlogTransform.cpp -o hyperlogTransform.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c inPolygon.cpp -o inPolygon.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c inPolytope.cpp -o inPolytope.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c logicleTransform.cpp -o logicleTransform.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c poly_centroid.cpp -o poly_centroid.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c sortBytes.cpp -o sortBytes.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c uint2double.cpp -o uint2double.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c zeroin.cpp -o zeroin.o
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 flowCore.so FastLogicle.o Hyperlog.o Logicle.o biexponential.o convertRawBytes.o cpp11.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o poly_centroid.o sortBytes.o uint2double.o zeroin.o /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/lib/libcytolib.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.so; fi
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/flowCore.buildbin-libdir/00LOCK-flowCore/00new/flowCore/libs
** R
** data
** 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 (flowCore)


>>>>>>> 
>>>>>>> FIXING LINKS FOR flowCore.buildbin-libdir/flowCore/libs/flowCore.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" "flowCore.buildbin-libdir/flowCore/libs/flowCore.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" "flowCore.buildbin-libdir/flowCore/libs/flowCore.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" "flowCore.buildbin-libdir/flowCore/libs/flowCore.so"