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BioC 2.13: CHECK report for Rchemcpp on zin1

This page was generated on 2014-04-05 09:48:43 -0700 (Sat, 05 Apr 2014).

Package 581/750HostnameOS / ArchBUILDCHECKBUILD BIN
Rchemcpp 2.0.2
Guenter Klambauer
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/Rchemcpp
Last Changed Rev: 86082 / Revision: 88450
Last Changed Date: 2014-02-04 15:36:04 -0800 (Tue, 04 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: Rchemcpp
Version: 2.0.2
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings Rchemcpp_2.0.2.tar.gz
StartedAt: 2014-04-05 03:24:21 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:25:59 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 98.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Rchemcpp.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/Rchemcpp.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ‘2.0.2’
* 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 ... [58s/59s] OK
* checking installed package size ... NOTE
  installed size is 12.3Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      9.0Mb
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘ChemmineR’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/Rchemcpp.Rcheck/00check.log’
for details.

Rchemcpp.Rcheck/00install.out:

* installing *source* package ‘Rchemcpp’ ...
** libs
make[1]: Entering directory `/home/biocbuild/bbs-2.13-bioc/meat/Rchemcpp.Rcheck/00_pkg_src/Rchemcpp/src/chemcpp/src'
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o constant.o constant.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o node.o node.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o atom.o atom.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o bond.o bond.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o cerror.o cerror.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o chemcpp.o chemcpp.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o datacontainer.o datacontainer.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o descriptor.o descriptor.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o elements.o elements.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o jlpioutils.o jlpioutils.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o kcfmolecule.o kcfmolecule.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o molecule.o molecule.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o moleculeset.o moleculeset.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o moleculeutils.o moleculeutils.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o ring.o ring.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o stringutils.o stringutils.cpp
g++ -shared -o ../../libchemcpp.dll -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
g++ -shared -o ../../libchemcpp.so -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
make[1]: Leaving directory `/home/biocbuild/bbs-2.13-bioc/meat/Rchemcpp.Rcheck/00_pkg_src/Rchemcpp/src/chemcpp/src'
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c Relements.cpp -o Relements.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c Rmolecule.cpp -o Rmolecule.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c Rmoleculeset.cpp -o Rmoleculeset.o
In file included from Rmoleculeset.cpp:2:0:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c spectrum3Dhelper.cpp -o spectrum3Dhelper.o
In file included from spectrum3Dhelper.h:38:0,
                 from spectrum3Dhelper.cpp:32:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp: In function ‘void gramSpectrum3D_self(SEXP, int, int, int, double, double, bool)’:
spectrum3Dhelper.cpp:74:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp: In function ‘void gramSpectrum3D_test(SEXP, int, int, int, double, double, bool)’:
spectrum3Dhelper.cpp:174:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp: In function ‘void gramComputeSpectrum3D_self(MoleculeSet*, int, int, int, std::vector<pathsInMol3D>*, std::vector<std::basic_string<char> >*, std::vector<int>*, bool)’:
spectrum3Dhelper.cpp:225:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp:241:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp:242:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp: In function ‘void gramComputeSpectrum3D_test(MoleculeSet*, MoleculeSet*, int, int, int, std::vector<pathsInMol3D>*, std::vector<pathsInMol3D>*, std::vector<std::basic_string<char> >*, std::vector<int>*, bool)’:
spectrum3Dhelper.cpp:279:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp:295:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp:296:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp: In function ‘void updatePaths3D(MoleculeSet*, std::string, int, std::vector<pathsInMol3D>*, std::vector<pathsInMol3D>*, int, int)’:
spectrum3Dhelper.cpp:384:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp:388:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp: In function ‘void updateGram3D_self(MoleculeSet*, std::vector<pathsInMol3D>*, int)’:
spectrum3Dhelper.cpp:445:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp:446:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp: In function ‘void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector<pathsInMol3D>*, std::vector<pathsInMol3D>*, int)’:
spectrum3Dhelper.cpp:488:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp:489:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp: In function ‘void updateSelfKernel3D(MoleculeSet*, std::vector<pathsInMol3D>*, int)’:
spectrum3Dhelper.cpp:530:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp: In function ‘void updateGram3D_self(MoleculeSet*, std::vector<pathsInMol3D>*, int)’:
spectrum3Dhelper.cpp:472:75: warning: ‘update’ may be used uninitialized in this function [-Wuninitialized]
spectrum3Dhelper.cpp: In function ‘void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector<pathsInMol3D>*, std::vector<pathsInMol3D>*, int)’:
spectrum3Dhelper.cpp:513:80: warning: ‘update’ may be used uninitialized in this function [-Wuninitialized]
spectrum3Dhelper.cpp: In function ‘void updateSelfKernel3D(MoleculeSet*, std::vector<pathsInMol3D>*, int)’:
spectrum3Dhelper.cpp:557:34: warning: ‘update’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c spectrumhelper.cpp -o spectrumhelper.o
In file included from spectrumhelper.h:38:0,
                 from spectrumhelper.cpp:32:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp: In function ‘void gramSpectrum_self(SEXP, int, int, double, bool, bool)’:
spectrumhelper.cpp:72:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:75:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp: In function ‘void gramSpectrum_test(SEXP, int, int, double, bool, bool)’:
spectrumhelper.cpp:130:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:133:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp: In function ‘void gramComputeSpectrum_self(MoleculeSet*, int, int, int, double, std::vector<pathsInMol>*, std::vector<std::basic_string<char> >*, std::vector<int>*, bool, bool)’:
spectrumhelper.cpp:161:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:188:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:189:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp: In function ‘void gramComputeSpectrum_test(MoleculeSet*, MoleculeSet*, int, int, int, double, std::vector<pathsInMol>*, std::vector<pathsInMol>*, std::vector<std::basic_string<char> >*, std::vector<int>*, bool, bool)’:
spectrumhelper.cpp:229:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:258:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:259:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp: In function ‘void updatePaths(MoleculeSet*, std::string, int, std::vector<pathsInMol>*, std::vector<pathsInMol>*, int, int)’:
spectrumhelper.cpp:368:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:372:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp: In function ‘void updateGram_self(MoleculeSet*, std::vector<pathsInMol>*, int, double, int)’:
spectrumhelper.cpp:453:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:455:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:467:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:468:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp: In function ‘void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector<pathsInMol>*, std::vector<pathsInMol>*, int, double, int)’:
spectrumhelper.cpp:518:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:520:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:528:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:530:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:543:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:544:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp: In function ‘void updateSelfKernel(MoleculeSet*, std::vector<pathsInMol>*, int, double, int)’:
spectrumhelper.cpp:592:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:594:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:606:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp: In function ‘void updateGram_self(MoleculeSet*, std::vector<pathsInMol>*, int, double, int)’:
spectrumhelper.cpp:499:75: warning: ‘update’ may be used uninitialized in this function [-Wuninitialized]
spectrumhelper.cpp: In function ‘void updateSelfKernel(MoleculeSet*, std::vector<pathsInMol>*, int, double, int)’:
spectrumhelper.cpp:630:34: warning: ‘update’ may be used uninitialized in this function [-Wuninitialized]
spectrumhelper.cpp: In function ‘void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector<pathsInMol>*, std::vector<pathsInMol>*, int, double, int)’:
spectrumhelper.cpp:570:80: warning: ‘update’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c subtreehelper.cpp -o subtreehelper.o
In file included from subtreehelper.h:37:0,
                 from subtreehelper.cpp:32:
Rmoleculeset.h: In member function ‘SEXPREC* Rmoleculeset::getMolByIndex(int)’:
Rmoleculeset.h:330:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp: In function ‘void gramSubtree_self(SEXP, double, int, bool, bool, bool, bool)’:
subtreehelper.cpp:59:6: warning: unused variable ‘depth’ [-Wunused-variable]
subtreehelper.cpp: In function ‘void gramSubtree_test(SEXP, double, int, bool, bool, bool, bool)’:
subtreehelper.cpp:138:6: warning: unused variable ‘depth’ [-Wunused-variable]
subtreehelper.cpp: In function ‘void initialize_extended(MoleculeSet*, std::vector<std::vector<std::vector<Nextatom> > >*)’:
subtreehelper.cpp:215:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp: In function ‘double subTreeKernel(Molecule*, Molecule*, std::vector<std::vector<Nextatom> >*, std::vector<std::vector<Nextatom> >*, int, double, bool, bool, bool)’:
subtreehelper.cpp:297:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp:304:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp:304:74: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp:321:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp:322:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp:350:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp: In function ‘void initialize_tuples(int)’:
subtreehelper.cpp:451:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp:457:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -shared -L/usr/local/lib -o Rchemcpp.so Relements.o Rmolecule.o Rmoleculeset.o spectrum3Dhelper.o spectrumhelper.o subtreehelper.o -L./ -lchemcpp -Wl,-rpath,/home/biocbuild/bbs-2.13-bioc/meat/Rchemcpp.Rcheck/Rchemcpp/libs -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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-package2.3120.0242.368
Rcpp_Rmolecule-class0.0560.0000.054
Rcpp_Rmoleculeset-class0.0080.0000.011
createRMolecule0.0040.0000.004
getMoleculeNamesFromSDF0.0120.0000.012
getMoleculePropertyFromSDF0.0080.0000.007
sd2gram0.8640.0040.871
sd2gram3Dpharma0.7760.0080.786
sd2gram3Dspectrum0.2120.0000.212
sd2gramSpectrum0.0320.0000.033
sd2gramSubtree0.2040.0160.220