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 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rchemcpp_2.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/Rchemcpp.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rchemcpp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rchemcpp’ version ‘2.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rchemcpp’ can be installed ... [61s/63s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
src/chemcpp/src/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
WARNING: There was 1 warning.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/Rchemcpp.Rcheck/00check.log’
for details.
* installing *source* package ‘Rchemcpp’ ...
** 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.Rcheck/Rchemcpp/libs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/Rchemcpp.Rcheck/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)