Guenter Klambauer
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Rchemcpp |
| Branch: master |
| Last Commit: 1e538d9 |
| Last Changed Date: 2019-01-04 13:46:16 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:08:02 -0400 (Tue, 09 Apr 2019).
| Package 1301/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rchemcpp 2.21.1 Guenter Klambauer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | [ OK ] | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: Rchemcpp |
| Version: 2.21.1 |
| Command: rm -rf Rchemcpp.buildbin-libdir && mkdir Rchemcpp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rchemcpp_2.21.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rchemcpp.buildbin-libdir |
| StartedAt: 2019-04-09 07:37:11 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 07:39:31 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 140.5 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rchemcpp_2.21.1.tgz |
| PackageFileSize: 1.08 MiB |
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### Running command:
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### rm -rf Rchemcpp.buildbin-libdir && mkdir Rchemcpp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rchemcpp_2.21.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rchemcpp.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rchemcpp.buildbin-libdir Rchemcpp_2.21.1.tar.gz'
>>>>>>>
* installing *source* package ‘Rchemcpp’ ...
** using staged installation
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++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o constant.o constant.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o node.o node.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o atom.o atom.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o bond.o bond.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o cerror.o cerror.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o chemcpp.o chemcpp.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o datacontainer.o datacontainer.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o descriptor.o descriptor.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o elements.o elements.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o jlpioutils.o jlpioutils.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o kcfmolecule.o kcfmolecule.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o molecule.o molecule.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o moleculeset.o moleculeset.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o moleculeutils.o moleculeutils.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o ring.o ring.cpp
clang++ -std=gnu++11 -Wall -g -O2 -w -fPIC -I../src/ -c -o stringutils.o stringutils.cpp
clang++ -std=gnu++11 -shared -o ../../libchemcpp.dll -Wall -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++ -std=gnu++11 -dynamiclib -o ../../libchemcpp.so -Wall -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./chemcpp/src -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Relements.cpp -o Relements.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./chemcpp/src -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./chemcpp/src -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./chemcpp/src -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./chemcpp/src -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./chemcpp/src -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -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++ -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/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-3.9-bioc/meat/Rchemcpp.buildbin-libdir/00LOCK-Rchemcpp/00new/Rchemcpp/libs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.buildbin-libdir/00LOCK-Rchemcpp/00new/Rchemcpp/libs
** R
** inst
** byte-compile and prepare 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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
install_name_tool -rpath /Users/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.buildbin-libdir/00LOCK-Rchemcpp/00new/Rchemcpp/libs /Users/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.buildbin-libdir/Rchemcpp/libs /Users/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.buildbin-libdir/00LOCK-Rchemcpp/00new/Rchemcpp/libs/Rchemcpp.so
NOTE: fixed rpath /Users/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.buildbin-libdir/00LOCK-Rchemcpp/00new/Rchemcpp/libs
WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* 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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/Resources/lib/libquadmath.0.dylib" "Rchemcpp.buildbin-libdir/Rchemcpp/libs//libchemcpp.so"