Package: Rchemcpp

Version: 2.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rchemcpp_2.16.0.tar.gz

StartedAt: 2018-04-12 08:23:14 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 08:25:45 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 151.0 seconds

RetCode: 0

Status:  OK

CheckDir: Rchemcpp.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rchemcpp_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Rchemcpp.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.16.0’
* 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 ... 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 ... NOTE
plotStruc: no visible global function definition for ‘lines’
plotStruc: no visible global function definition for ‘points’
plotStruc: no visible global function definition for ‘text’
plot,SDFset: no visible global function definition for ‘par’
Undefined global functions or variables:
  lines par points text
Consider adding
  importFrom("graphics", "lines", "par", "points", "text")
to your NAMESPACE file.
* 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 shell scripts ... 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 ... NOTE
GNU make is a SystemRequirements.
* 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 ... 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

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/Rchemcpp.Rcheck/00check.log’
for details.

* installing *source* package ‘Rchemcpp’ ...
** libs
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o constant.o constant.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o node.o node.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o atom.o atom.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o bond.o bond.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o cerror.o cerror.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o chemcpp.o chemcpp.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o datacontainer.o datacontainer.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o descriptor.o descriptor.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o elements.o elements.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o jlpioutils.o jlpioutils.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o kcfmolecule.o kcfmolecule.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o molecule.o molecule.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o moleculeset.o moleculeset.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o moleculeutils.o moleculeutils.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o ring.o ring.cpp
clang++  -Wall -g -O2  -w -fPIC -I../src/   -c -o stringutils.o stringutils.cpp
clang++  -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++  -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++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Relements.cpp -o Relements.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I"/Library/Frameworks/R.framework/Versions/3.4/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++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I"/Library/Frameworks/R.framework/Versions/3.4/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++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I"/Library/Frameworks/R.framework/Versions/3.4/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++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I"/Library/Frameworks/R.framework/Versions/3.4/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++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I"/Library/Frameworks/R.framework/Versions/3.4/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++ -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-3.6-bioc/meat/Rchemcpp.Rcheck/Rchemcpp/libs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-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)

name	user	system	elapsed
Rchemcpp-package	2.117	0.059	2.237
Rcpp_Rmolecule-class	0.002	0.000	0.003
Rcpp_Rmoleculeset-class	0.004	0.000	0.004
createRMolecule	0.002	0.000	0.003
getMoleculeNamesFromSDF	0.011	0.000	0.011
getMoleculePropertyFromSDF	0.003	0.001	0.003
sd2gram	0.754	0.017	0.786
sd2gram3Dpharma	0.683	0.015	0.720
sd2gram3Dspectrum	0.324	0.002	0.338
sd2gramSpectrum	0.138	0.002	0.146
sd2gramSubtree	0.350	0.010	0.372