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BioC 3.2: CHECK report for Rchemcpp on perceval

This page was generated on 2015-10-27 17:35:46 -0400 (Tue, 27 Oct 2015).

Package 852/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rchemcpp 2.8.0
Guenter Klambauer
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Rchemcpp
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rchemcpp
Version: 2.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rchemcpp_2.8.0.tar.gz
StartedAt: 2015-10-27 11:30:15 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 11:32:16 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 121.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Rchemcpp.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rchemcpp_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Rchemcpp.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.8.0’
* 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 ... [57s/62s] 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 ... 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 ... [9s/9s] 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/Rchemcpp.Rcheck/00check.log’
for details.

Rchemcpp.Rcheck/00install.out:

* installing *source* package ‘Rchemcpp’ ...
** libs
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o constant.o constant.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o node.o node.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o atom.o atom.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o bond.o bond.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o cerror.o cerror.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o chemcpp.o chemcpp.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o datacontainer.o datacontainer.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o descriptor.o descriptor.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o elements.o elements.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o jlpioutils.o jlpioutils.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o kcfmolecule.o kcfmolecule.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o molecule.o molecule.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o moleculeset.o moleculeset.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o moleculeutils.o moleculeutils.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o ring.o ring.cpp
llvm-g++-4.2 -arch x86_64 -mtune=core2 -g -O2 -Wall  -w -fPIC -I../src/   -c -o stringutils.o stringutils.cpp
llvm-g++-4.2 -arch x86_64 -shared -o ../../libchemcpp.dll -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -dynamiclib -o ../../libchemcpp.so -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Relements.cpp -o Relements.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Rmolecule.cpp -o Rmolecule.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Rmoleculeset.cpp -o Rmoleculeset.o
In file included from Rmoleculeset.cpp:2:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c spectrum3Dhelper.cpp -o spectrum3Dhelper.o
In file included from spectrum3Dhelper.h:38,
                 from spectrum3Dhelper.cpp:32:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void gramSpectrum3D_self(SEXPREC*, int, int, int, double, double, bool)’:
spectrum3Dhelper.cpp:74: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void gramSpectrum3D_test(SEXPREC*, int, int, int, double, double, bool)’:
spectrum3Dhelper.cpp:174: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void gramComputeSpectrum3D_self(MoleculeSet*, int, int, int, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, std::vector<int, std::allocator<int> >*, bool)’:
spectrum3Dhelper.cpp:225: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:241: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:242: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void gramComputeSpectrum3D_test(MoleculeSet*, MoleculeSet*, int, int, int, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, std::vector<int, std::allocator<int> >*, bool)’:
spectrum3Dhelper.cpp:279: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:295: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:296: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void updatePaths3D(MoleculeSet*, std::string, int, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, int, int)’:
spectrum3Dhelper.cpp:384: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:388: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void updateGram3D_self(MoleculeSet*, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, int)’:
spectrum3Dhelper.cpp:445: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:446: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, int)’:
spectrum3Dhelper.cpp:488: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp:489: warning: comparison between signed and unsigned integer expressions
spectrum3Dhelper.cpp: In function ‘void updateSelfKernel3D(MoleculeSet*, std::vector<pathsInMol3D, std::allocator<pathsInMol3D> >*, int)’:
spectrum3Dhelper.cpp:530: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c spectrumhelper.cpp -o spectrumhelper.o
In file included from spectrumhelper.h:38,
                 from spectrumhelper.cpp:32:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void gramSpectrum_self(SEXPREC*, int, int, double, bool, bool)’:
spectrumhelper.cpp:72: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:75: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void gramSpectrum_test(SEXPREC*, int, int, double, bool, bool)’:
spectrumhelper.cpp:130: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:133: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void gramComputeSpectrum_self(MoleculeSet*, int, int, int, double, std::vector<pathsInMol, std::allocator<pathsInMol> >*, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, std::vector<int, std::allocator<int> >*, bool, bool)’:
spectrumhelper.cpp:161: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:188: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:189: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void gramComputeSpectrum_test(MoleculeSet*, MoleculeSet*, int, int, int, double, std::vector<pathsInMol, std::allocator<pathsInMol> >*, std::vector<pathsInMol, std::allocator<pathsInMol> >*, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, std::vector<int, std::allocator<int> >*, bool, bool)’:
spectrumhelper.cpp:229: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:258: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:259: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void updatePaths(MoleculeSet*, std::string, int, std::vector<pathsInMol, std::allocator<pathsInMol> >*, std::vector<pathsInMol, std::allocator<pathsInMol> >*, int, int)’:
spectrumhelper.cpp:368: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:372: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void updateGram_self(MoleculeSet*, std::vector<pathsInMol, std::allocator<pathsInMol> >*, int, double, int)’:
spectrumhelper.cpp:453: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:455: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:467: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:468: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector<pathsInMol, std::allocator<pathsInMol> >*, std::vector<pathsInMol, std::allocator<pathsInMol> >*, int, double, int)’:
spectrumhelper.cpp:518: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:520: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:528: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:530: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:543: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:544: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp: In function ‘void updateSelfKernel(MoleculeSet*, std::vector<pathsInMol, std::allocator<pathsInMol> >*, int, double, int)’:
spectrumhelper.cpp:592: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:594: warning: comparison between signed and unsigned integer expressions
spectrumhelper.cpp:606: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c subtreehelper.cpp -o subtreehelper.o
In file included from subtreehelper.h:37,
                 from subtreehelper.cpp:32:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp: In function ‘void gramSubtree_self(SEXPREC*, double, int, bool, bool, bool, bool)’:
subtreehelper.cpp:59: warning: unused variable ‘depth’
subtreehelper.cpp: In function ‘void gramSubtree_test(SEXPREC*, double, int, bool, bool, bool, bool)’:
subtreehelper.cpp:138: warning: unused variable ‘depth’
subtreehelper.cpp: In function ‘void initialize_extended(MoleculeSet*, std::vector<std::vector<std::vector<Nextatom, std::allocator<Nextatom> >, std::allocator<std::vector<Nextatom, std::allocator<Nextatom> > > >, std::allocator<std::vector<std::vector<Nextatom, std::allocator<Nextatom> >, std::allocator<std::vector<Nextatom, std::allocator<Nextatom> > > > > >*)’:
subtreehelper.cpp:215: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp: In function ‘double subTreeKernel(Molecule*, Molecule*, std::vector<std::vector<Nextatom, std::allocator<Nextatom> >, std::allocator<std::vector<Nextatom, std::allocator<Nextatom> > > >*, std::vector<std::vector<Nextatom, std::allocator<Nextatom> >, std::allocator<std::vector<Nextatom, std::allocator<Nextatom> > > >*, int, double, bool, bool, bool)’:
subtreehelper.cpp:297: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp:304: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp:304: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp:321: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp:322: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp:350: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp: In function ‘void initialize_tuples(int)’:
subtreehelper.cpp:451: warning: comparison between signed and unsigned integer expressions
subtreehelper.cpp:457: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -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 -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-3.2-bioc/meat/Rchemcpp.Rcheck/Rchemcpp/libs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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)

Rchemcpp.Rcheck/Rchemcpp-Ex.timings:

nameusersystemelapsed
Rchemcpp-package3.5940.0753.670
Rcpp_Rmolecule-class0.0030.0000.003
Rcpp_Rmoleculeset-class0.0110.0000.012
createRMolecule0.0040.0000.005
getMoleculeNamesFromSDF0.0100.0010.010
getMoleculePropertyFromSDF0.0030.0000.004
sd2gram1.4290.0131.443
sd2gram3Dpharma1.0190.0221.040
sd2gram3Dspectrum0.4550.0030.458
sd2gramSpectrum0.0330.0020.036
sd2gramSubtree0.3370.0120.348