BioC 2.14: BUILD BIN report for NetPathMiner on petty

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### Running command:
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###   rm -rf NetPathMiner.buildbin-libdir && mkdir NetPathMiner.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NetPathMiner_1.0.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R NetPathMiner.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=NetPathMiner.buildbin-libdir NetPathMiner_1.0.4.tar.gz'
>>>>>>> 

* installing *source* package ‘NetPathMiner’ ...
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
checking for gcc... llvm-gcc-4.2 -arch x86_64 -std=gnu99
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 llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... llvm-gcc-4.2 -arch x86_64 -std=gnu99 -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... yes
untarring boost include tree...
libSBML found, finding configuration...
pkg-config tool found
libsbml.pc found. Using pkg-config to extract it.
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fPIC  -mtune=core2 -g -O2 -Wall  -c PathRanker.cpp -o PathRanker.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c handlesegfault.c -o handlesegfault.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c hme3m.c -o hme3m.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init.c -o init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fPIC  -mtune=core2 -g -O2 -Wall  -c kgml_interface.cpp -o kgml_interface.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fPIC  -mtune=core2 -g -O2 -Wall  -c methods.cpp -o methods.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fPIC  -mtune=core2 -g -O2 -Wall  -c pathScope.cpp -o pathScope.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fPIC  -mtune=core2 -g -O2 -Wall  -c sbml_interface.cpp -o sbml_interface.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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 -lsbml -lxml2 -lxml2 -lz -lpthread -licucore -lm -lsbml -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/NetPathMiner.buildbin-libdir/NetPathMiner/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* 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/3.1/Resources/lib/libgcc_s.1.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs//NetPathMiner.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.2.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs//NetPathMiner.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.5.2.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs//NetPathMiner.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs//NetPathMiner.so"
BioC 2.14: BUILD BIN report for NetPathMiner on petty

Summary

Command output
