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BioC 3.0: BUILD BIN report for Rchemcpp on oaxaca

This page was generated on 2015-04-10 10:07:42 -0700 (Fri, 10 Apr 2015).

Package 725/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rchemcpp 2.4.0
Guenter Klambauer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/Rchemcpp
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS [ OK ]

Summary

Package: Rchemcpp
Version: 2.4.0
Command: rm -rf Rchemcpp.buildbin-libdir && mkdir Rchemcpp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rchemcpp_2.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rchemcpp.buildbin-libdir
StartedAt: 2015-04-10 04:52:08 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:53:12 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 64.4 seconds
RetCode: 0
Status:  OK 
PackageFile: Rchemcpp_2.4.0.tgz
PackageFileSize: 1.011 MiB

Command output

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###
### Running command:
###
###   rm -rf Rchemcpp.buildbin-libdir && mkdir Rchemcpp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rchemcpp_2.4.0.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_2.4.0.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
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o constant.o constant.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o node.o node.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o atom.o atom.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o bond.o bond.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o cerror.o cerror.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o chemcpp.o chemcpp.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o datacontainer.o datacontainer.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o descriptor.o descriptor.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o elements.o elements.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o jlpioutils.o jlpioutils.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o kcfmolecule.o kcfmolecule.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o molecule.o molecule.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o moleculeset.o moleculeset.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o moleculeutils.o moleculeutils.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o ring.o ring.cpp
clang++ -Wall -mtune=core2 -g -O2  -w -fPIC -I../src/   -c -o stringutils.o stringutils.cpp
clang++ -shared -o ../../libchemcpp.dll -Wall -mtune=core2 -g -O2  -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
clang++ -dynamiclib -o ../../libchemcpp.so -Wall -mtune=core2 -g -O2  -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
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Relements.cpp -o Relements.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Rmolecule.cpp -o Rmolecule.o
In file included from Rmolecule.cpp:2:
./Rmolecule.h:14:7: warning: 'Rmolecule::addAtom' hides overloaded virtual function [-Woverloaded-virtual]
        void addAtom(string aSymbol)
             ^
./chemcpp/src/molecule.h:133:16: note: hidden overloaded virtual function 'Molecule::addAtom' declared here: different number of parameters (2 vs 1)
        virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
                      ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Rmoleculeset.cpp -o Rmoleculeset.o
In file included from Rmoleculeset.cpp:2:
In file included from ./Rmoleculeset.h:8:
./Rmolecule.h:14:7: warning: 'Rmolecule::addAtom' hides overloaded virtual function [-Woverloaded-virtual]
        void addAtom(string aSymbol)
             ^
./chemcpp/src/molecule.h:133:16: note: hidden overloaded virtual function 'Molecule::addAtom' declared here: different number of parameters (2 vs 1)
        virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
                      ^
In file included from Rmoleculeset.cpp:2:
In file included from ./Rmoleculeset.h:10:
In file included from ./chemcpp/src/moleculeset.h:39:
./chemcpp/src/kcfmolecule.h:61:16: warning: 'KCFMolecule::addAtom' hides overloaded virtual function [-Woverloaded-virtual]
        virtual Atom* addAtom(string aSymbol) throw( CError );
                      ^
./chemcpp/src/molecule.h:133:16: note: hidden overloaded virtual function 'Molecule::addAtom' declared here: different number of parameters (2 vs 1)
        virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
                      ^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c spectrum3Dhelper.cpp -o spectrum3Dhelper.o
In file included from spectrum3Dhelper.cpp:32:
In file included from ./spectrum3Dhelper.h:38:
In file included from ./Rmoleculeset.h:8:
./Rmolecule.h:14:7: warning: 'Rmolecule::addAtom' hides overloaded virtual function [-Woverloaded-virtual]
        void addAtom(string aSymbol)
             ^
./chemcpp/src/molecule.h:133:16: note: hidden overloaded virtual function 'Molecule::addAtom' declared here: different number of parameters (2 vs 1)
        virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
                      ^
In file included from spectrum3Dhelper.cpp:32:
In file included from ./spectrum3Dhelper.h:38:
In file included from ./Rmoleculeset.h:10:
In file included from ./chemcpp/src/moleculeset.h:39:
./chemcpp/src/kcfmolecule.h:61:16: warning: 'KCFMolecule::addAtom' hides overloaded virtual function [-Woverloaded-virtual]
        virtual Atom* addAtom(string aSymbol) throw( CError );
                      ^
./chemcpp/src/molecule.h:133:16: note: hidden overloaded virtual function 'Molecule::addAtom' declared here: different number of parameters (2 vs 1)
        virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
                      ^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c spectrumhelper.cpp -o spectrumhelper.o
In file included from spectrumhelper.cpp:32:
In file included from ./spectrumhelper.h:38:
In file included from ./Rmoleculeset.h:8:
./Rmolecule.h:14:7: warning: 'Rmolecule::addAtom' hides overloaded virtual function [-Woverloaded-virtual]
        void addAtom(string aSymbol)
             ^
./chemcpp/src/molecule.h:133:16: note: hidden overloaded virtual function 'Molecule::addAtom' declared here: different number of parameters (2 vs 1)
        virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
                      ^
In file included from spectrumhelper.cpp:32:
In file included from ./spectrumhelper.h:38:
In file included from ./Rmoleculeset.h:10:
In file included from ./chemcpp/src/moleculeset.h:39:
./chemcpp/src/kcfmolecule.h:61:16: warning: 'KCFMolecule::addAtom' hides overloaded virtual function [-Woverloaded-virtual]
        virtual Atom* addAtom(string aSymbol) throw( CError );
                      ^
./chemcpp/src/molecule.h:133:16: note: hidden overloaded virtual function 'Molecule::addAtom' declared here: different number of parameters (2 vs 1)
        virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
                      ^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c subtreehelper.cpp -o subtreehelper.o
In file included from subtreehelper.cpp:32:
In file included from ./subtreehelper.h:37:
In file included from ./Rmoleculeset.h:8:
./Rmolecule.h:14:7: warning: 'Rmolecule::addAtom' hides overloaded virtual function [-Woverloaded-virtual]
        void addAtom(string aSymbol)
             ^
./chemcpp/src/molecule.h:133:16: note: hidden overloaded virtual function 'Molecule::addAtom' declared here: different number of parameters (2 vs 1)
        virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
                      ^
In file included from subtreehelper.cpp:32:
In file included from ./subtreehelper.h:37:
In file included from ./Rmoleculeset.h:10:
In file included from ./chemcpp/src/moleculeset.h:39:
./chemcpp/src/kcfmolecule.h:61:16: warning: 'KCFMolecule::addAtom' hides overloaded virtual function [-Woverloaded-virtual]
        virtual Atom* addAtom(string aSymbol) throw( CError );
                      ^
./chemcpp/src/molecule.h:133:16: note: hidden overloaded virtual function 'Molecule::addAtom' declared here: different number of parameters (2 vs 1)
        virtual Atom* addAtom( string aSymbol, bool resetSSSR = true ) throw( CError );
                      ^
subtreehelper.cpp:59:6: warning: unused variable 'depth' [-Wunused-variable]
        int depth = -1;
            ^
subtreehelper.cpp:138:6: warning: unused variable 'depth' [-Wunused-variable]
        int depth = -1;
            ^
4 warnings generated.
clang++ -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 Rchemcpp.so Relements.o Rmolecule.o Rmoleculeset.o spectrum3Dhelper.o spectrumhelper.o subtreehelper.o -L./ -lchemcpp -Wl,-rpath,/Users/biocbuild/bbs-3.0-bioc/meat/Rchemcpp.buildbin-libdir/Rchemcpp/libs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-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/3.1/Resources/lib/libgcc_s.1.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//Rchemcpp.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.3.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//Rchemcpp.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/lib/libreadline.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//Rchemcpp.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libquadmath.0.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/3.1/Resources/lib/libgcc_s.1.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//libchemcpp.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.3.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//libchemcpp.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/lib/libreadline.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//libchemcpp.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libquadmath.0.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//libchemcpp.so"