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CHECK report for Rchemcpp on celaya2

This page was generated on 2019-04-09 13:08:02 -0400 (Tue, 09 Apr 2019).

Package 1301/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rchemcpp 2.21.1
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  ERROR  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: Rchemcpp
Version: 2.21.1
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_2.21.1.tar.gz
StartedAt: 2019-04-09 04:48:07 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:49:22 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 75.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Rchemcpp.Rcheck
Warnings: 1

Command output

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### Running 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_2.21.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.21.1’
* 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: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Users/biocbuild/bbs-3.9-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-3.9-bioc/meat/Rchemcpp.Rcheck/00check.log’
for details.



Installation output

Rchemcpp.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rchemcpp
###
##############################################################################
##############################################################################


* 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" -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,/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
** 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
** testing if installed package keeps a record of temporary installation path
* DONE (Rchemcpp)

Tests output


Example timings

Rchemcpp.Rcheck/Rchemcpp-Ex.timings

nameusersystemelapsed
Rchemcpp-package2.2770.1512.440
Rcpp_Rmolecule-class0.0030.0010.005
Rcpp_Rmoleculeset-class0.0060.0010.008
createRMolecule0.0050.0000.005
getMoleculeNamesFromSDF0.0060.0010.006
getMoleculePropertyFromSDF0.0030.0010.003
sd2gram0.6080.0200.628
sd2gram3Dpharma0.7320.0500.782
sd2gram3Dspectrum0.2070.0060.215
sd2gramSpectrum0.0270.0040.032
sd2gramSubtree0.3310.0300.361