##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf NetPathMiner.buildbin-libdir && mkdir NetPathMiner.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NetPathMiner_1.30.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R NetPathMiner.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=NetPathMiner.buildbin-libdir NetPathMiner_1.30.0.tar.gz'
>>>>>>> 

* installing *source* package ‘NetPathMiner’ ...
** using staged installation
removing boost headers...
restoring Makevars.in file...
mv: _Makevars.in_: No such file or directory
rm: Makevars: No such file or directory
removing compiled code...
rm: *.o: No such file or directory
'config' variable 'CPP' is defunct
checking for gcc... clang -mmacosx-version-min=10.13
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 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... no
untarring boost include tree...
SBML not found.
libXML2 found
checking for xml2-config... /usr/local/opt/libxml2/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/usr/local/Cellar/libxml2/2.9.10_2/include/libxml2 -fPIC  -Wall -g -O2  -c PathRanker.cpp -o PathRanker.o
In file included from PathRanker.cpp:23:
In file included from /usr/local/include/boost/graph/graph_utility.hpp:26:
In file included from /usr/local/include/boost/detail/algorithm.hpp:33:
/usr/local/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/usr/local/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.")
                                    ^
/usr/local/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>:44:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from PathRanker.cpp:25:
/usr/local/include/boost/pending/relaxed_heap.hpp:9:2: warning: "Use of relaxed_heap is depreciated; please use the standard heap functions." [-W#warnings]
#warning \
 ^
/usr/local/include/boost/pending/relaxed_heap.hpp:15:1: warning: This header is deprecated. Use the standard heap functions instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("the standard heap functions")
^
/usr/local/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.")
                                    ^
/usr/local/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>:32:2: note: expanded from here
 message("This header is deprecated. Use " "the standard heap functions" " instead.")
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c handlesegfault.c -o handlesegfault.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hme3m.c -o hme3m.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/usr/local/Cellar/libxml2/2.9.10_2/include/libxml2 -fPIC  -Wall -g -O2  -c kgml_interface.cpp -o kgml_interface.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/usr/local/Cellar/libxml2/2.9.10_2/include/libxml2 -fPIC  -Wall -g -O2  -c methods.cpp -o methods.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/usr/local/Cellar/libxml2/2.9.10_2/include/libxml2 -fPIC  -Wall -g -O2  -c pathScope.cpp -o pathScope.o
In file included from pathScope.cpp:28:
In file included from /usr/local/include/boost/graph/graph_utility.hpp:26:
In file included from /usr/local/include/boost/detail/algorithm.hpp:33:
/usr/local/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/usr/local/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.")
                                    ^
/usr/local/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>:56:2: note: expanded from here
 message("This header is deprecated. Use " "<iterator>" " instead.")
 ^
In file included from pathScope.cpp:30:
/usr/local/include/boost/pending/relaxed_heap.hpp:9:2: warning: "Use of relaxed_heap is depreciated; please use the standard heap functions." [-W#warnings]
#warning \
 ^
/usr/local/include/boost/pending/relaxed_heap.hpp:15:1: warning: This header is deprecated. Use the standard heap functions instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("the standard heap functions")
^
/usr/local/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.")
                                    ^
/usr/local/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>:34:2: note: expanded from here
 message("This header is deprecated. Use " "the standard heap functions" " instead.")
 ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I . -I/usr/local/include -DHAVE_XML -I/usr/local/Cellar/libxml2/2.9.10_2/include/libxml2 -fPIC  -Wall -g -O2  -c sbml_interface.cpp -o sbml_interface.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 NetPathMiner.so PathRanker.o handlesegfault.o hme3m.o init.o kgml_interface.o methods.o pathScope.o sbml_interface.o -lxml2 -L/usr/local/Cellar/libxml2/2.9.10_2/lib -lxml2 -lz -lpthread -liconv -lm -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.14-bioc/meat/NetPathMiner.buildbin-libdir/00LOCK-NetPathMiner/00new/NetPathMiner/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 (NetPathMiner)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so"