##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf Rchemcpp.buildbin-libdir && mkdir Rchemcpp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rchemcpp_2.8.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rchemcpp.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rchemcpp.buildbin-libdir Rchemcpp_2.8.0.tar.gz'
>>>>>>>
* installing *source* package ‘Rchemcpp’ ...
rm: ./src/*.o: No such file or directory
rm: ./src/*.so: No such file or directory
rm: ./src/*.dll: No such file or directory
rm: ./src/chemcpp/src/*.o: No such file or directory
** libs
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o constant.o constant.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o node.o node.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o atom.o atom.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o bond.o bond.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o cerror.o cerror.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o chemcpp.o chemcpp.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o datacontainer.o datacontainer.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o descriptor.o descriptor.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o elements.o elements.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o jlpioutils.o jlpioutils.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o kcfmolecule.o kcfmolecule.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o molecule.o molecule.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o moleculeset.o moleculeset.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o moleculeutils.o moleculeutils.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o ring.o ring.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ -c -o stringutils.o stringutils.cpp
llvm-g++-4.2 -arch x86_64 -shared -o ../../libchemcpp.dll -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ constant.o node.o atom.o bond.o cerror.o chemcpp.o datacontainer.o descriptor.o elements.o jlpioutils.o kcfmolecule.o molecule.o moleculeset.o moleculeutils.o ring.o stringutils.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -o ../../libchemcpp.so -mtune=core2 -g -O2 -Wall -w -fPIC -I../src/ constant.o node.o atom.o bond.o cerror.o chemcpp.o datacontainer.o descriptor.o elements.o jlpioutils.o kcfmolecule.o molecule.o moleculeset.o moleculeutils.o ring.o stringutils.o -Wl,-install_name -Wl,@loader_path/libchemcpp.so
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c Relements.cpp -o Relements.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c Rmolecule.cpp -o Rmolecule.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c Rmoleculeset.cpp -o Rmoleculeset.o
In file included from Rmoleculeset.cpp:2:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c spectrum3Dhelper.cpp -o spectrum3Dhelper.o
In file included from spectrum3Dhelper.h:38,
from spectrum3Dhelper.cpp:32:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void gramSpectrum3D_self(SEXPREC*, int, int, int, double, double, bool)’:
spectrum3Dhelper.cpp:74: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void gramSpectrum3D_test(SEXPREC*, int, int, int, double, double, bool)’:
spectrum3Dhelper.cpp:174: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void gramComputeSpectrum3D_self(MoleculeSet*, int, int, int, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, std::vector<int, std::allocator<int> >*, bool)’:
spectrum3Dhelper.cpp:225: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:241: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:242: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void gramComputeSpectrum3D_test(MoleculeSet*, MoleculeSet*, int, int, int, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, std::vector<int, std::allocator<int> >*, bool)’:
spectrum3Dhelper.cpp:279: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:295: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:296: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void updatePaths3D(MoleculeSet*, std::string, int, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, int, int)’:
spectrum3Dhelper.cpp:384: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:388: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void updateGram3D_self(MoleculeSet*, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, int)’:
spectrum3Dhelper.cpp:445: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:446: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, int)’:
spectrum3Dhelper.cpp:488: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:489: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void updateSelfKernel3D(MoleculeSet*, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, int)’:
spectrum3Dhelper.cpp:530: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c spectrumhelper.cpp -o spectrumhelper.o
In file included from spectrumhelper.h:38,
from spectrumhelper.cpp:32:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void gramSpectrum_self(SEXPREC*, int, int, double, bool, bool)’:
spectrumhelper.cpp:72: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:75: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void gramSpectrum_test(SEXPREC*, int, int, double, bool, bool)’:
spectrumhelper.cpp:130: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:133: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void gramComputeSpectrum_self(MoleculeSet*, int, int, int, double, std::vector<pathsInMol, std::allocator<pathsInMol> >*, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, std::vector<int, std::allocator<int> >*, bool, bool)’:
spectrumhelper.cpp:161: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:188: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:189: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void gramComputeSpectrum_test(MoleculeSet*, MoleculeSet*, int, int, int, double, std::vector<pathsInMol, std::allocator<pathsInMol> >*, std::vector<pathsInMol, std::allocator<pathsInMol> >*, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, std::vector<int, std::allocator<int> >*, bool, bool)’:
spectrumhelper.cpp:229: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:258: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:259: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void updatePaths(MoleculeSet*, std::string, int, std::vector<pathsInMol, std::allocator<pathsInMol> >*, std::vector<pathsInMol, std::allocator<pathsInMol> >*, int, int)’:
spectrumhelper.cpp:368: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:372: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void updateGram_self(MoleculeSet*, std::vector<pathsInMol, std::allocator<pathsInMol> >*, int, double, int)’:
spectrumhelper.cpp:453: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:455: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:467: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:468: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector<pathsInMol, std::allocator<pathsInMol> >*, std::vector<pathsInMol, std::allocator<pathsInMol> >*, int, double, int)’:
spectrumhelper.cpp:518: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:520: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:528: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:530: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:543: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:544: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void updateSelfKernel(MoleculeSet*, std::vector<pathsInMol, std::allocator<pathsInMol> >*, int, double, int)’:
spectrumhelper.cpp:592: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:594: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:606: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c subtreehelper.cpp -o subtreehelper.o
In file included from subtreehelper.h:37,
from subtreehelper.cpp:32:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp: In function ‘void gramSubtree_self(SEXPREC*, double, int, bool, bool, bool, bool)’:
subtreehelper.cpp:59: warning: unused variable ‘depth’
subtreehelper.cpp: In function ‘void gramSubtree_test(SEXPREC*, double, int, bool, bool, bool, bool)’:
subtreehelper.cpp:138: warning: unused variable ‘depth’
subtreehelper.cpp: In function ‘void initialize_extended(MoleculeSet*, std::vector<std::vector<std::vector<Nextatom, std::allocator<Nextatom> >, std::allocator<std::vector<Nextatom, std::allocator<Nextatom> > > >, std::allocator<std::vector<std::vector<Nextatom, std::allocator<Nextatom> >, std::allocator<std::vector<Nextatom, std::allocator<Nextatom> > > > > >*)’:
subtreehelper.cpp:215: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp: In function ‘double subTreeKernel(Molecule*, Molecule*, std::vector<std::vector<Nextatom, std::allocator<Nextatom> >, std::allocator<std::vector<Nextatom, std::allocator<Nextatom> > > >*, std::vector<std::vector<Nextatom, std::allocator<Nextatom> >, std::allocator<std::vector<Nextatom, std::allocator<Nextatom> > > >*, int, double, bool, bool, bool)’:
subtreehelper.cpp:297: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp:304: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp:304: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp:321: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp:322: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp:350: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp: In function ‘void initialize_tuples(int)’:
subtreehelper.cpp:451: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp:457: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o Rchemcpp.so Relements.o Rmolecule.o Rmoleculeset.o spectrum3Dhelper.o spectrumhelper.o subtreehelper.o -L./ -lchemcpp -Wl,-rpath,/Users/biocbuild/bbs-3.2-bioc/meat/Rchemcpp.buildbin-libdir/Rchemcpp/libs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/Rchemcpp.buildbin-libdir/Rchemcpp/libs
** R
** inst
** preparing package for lazy loading
in method for ‘length’ with signature ‘"Rcpp_Rmoleculeset"’: no definition for class “Rcpp_Rmoleculeset”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rchemcpp)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rchemcpp.buildbin-libdir/Rchemcpp/libs//Rchemcpp.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//Rchemcpp.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.2.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//Rchemcpp.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//Rchemcpp.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//Rchemcpp.so"
>>>>>>>
>>>>>>> FIXING LINKS FOR Rchemcpp.buildbin-libdir/Rchemcpp/libs//libchemcpp.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//libchemcpp.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.2.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//libchemcpp.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//libchemcpp.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//libchemcpp.so"
