Package: Rchemcpp

Version: 2.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rchemcpp.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rchemcpp_2.24.0.tar.gz

StartedAt: 2020-04-15 05:00:01 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:01:07 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 65.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Rchemcpp.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rchemcpp.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rchemcpp_2.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/Rchemcpp.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.24.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'Rchemcpp' is deprecated and will be removed from Bioconductor
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/Rchemcpp.Rcheck/00install.out’ for details.
* 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 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rchemcpp/libs/libchemcpp.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
  Found ‘_exit’, possibly from ‘exit’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/Rchemcpp.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rchemcpp
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Rchemcpp’ ...
** using staged installation
** 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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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,/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rchemcpp/00new/Rchemcpp/libs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/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
Warning: Package 'Rchemcpp' is deprecated and will be removed from Bioconductor
  version 3.11
** checking absolute paths in shared objects and dynamic libraries
install_name_tool -rpath '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rchemcpp/00new/Rchemcpp/libs' '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rchemcpp/libs' '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rchemcpp/00new/Rchemcpp/libs/Rchemcpp.so'
NOTE: fixed rpath /Library/Frameworks/R.framework/Versions/3.6/Resources/library/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
Warning: Package 'Rchemcpp' is deprecated and will be removed from Bioconductor
  version 3.11
** testing if installed package keeps a record of temporary installation path
* DONE (Rchemcpp)

name	user	system	elapsed
Rchemcpp-package	2.140	0.071	2.244
Rcpp_Rmolecule-class	0.002	0.000	0.002
Rcpp_Rmoleculeset-class	0.005	0.001	0.005
createRMolecule	0.004	0.000	0.005
getMoleculeNamesFromSDF	0.008	0.001	0.008
getMoleculePropertyFromSDF	0.002	0.001	0.002
sd2gram	0.757	0.013	0.775
sd2gram3Dpharma	0.732	0.019	0.758
sd2gram3Dspectrum	0.227	0.003	0.231
sd2gramSpectrum	0.035	0.002	0.038
sd2gramSubtree	0.263	0.010	0.274