BioC 3.2: CHECK report for ChemmineOB on oaxaca

Package: ChemmineOB

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChemmineOB_1.8.0.tar.gz

StartedAt: 2015-10-27 02:06:31 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:09:06 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 154.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ChemmineOB.Rcheck

Warnings: 2

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChemmineOB_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChemmineOB.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChemmineOB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineOB’ version ‘1.8.0’
* 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 ‘ChemmineOB’ can be installed ... [50s/69s] OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R                1.3Mb
    libs             3.0Mb
    openbabel_data   2.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ChemmineR’
A package should be listed in only one of these fields.
* 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
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘Rcpp’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
copyToC: no visible global function definition for ‘RSWIG_createNewRef’
copyToC,OpenBabel::CharPtrLess: no visible global function definition
  for ‘RSWIG_createNewRef’
copyToC,OpenBabel::DoubleType: no visible global function definition
  for ‘RSWIG_createNewRef’
copyToC,OpenBabel::FptIndexHeader: no visible global function
  definition for ‘RSWIG_createNewRef’
copyToC,OpenBabel::LineSearchType: no visible global function
  definition for ‘RSWIG_createNewRef’
copyToC,std::pair<(unsigned int,unsigned int)>: no visible global
  function definition for ‘RSWIG_createNewRef’
copyToC,stringp: no visible global function definition for
  ‘RSWIG_createNewRef’
delete,_p_OpenBabel__AliasData: no visible global function definition
  for ‘delete_OpenBabel__AliasData’
delete,_p_OpenBabel__CharPtrLess: no visible global function definition
  for ‘delete_OpenBabel__CharPtrLess’
delete,_p_OpenBabel__DoubleType: no visible global function definition
  for ‘delete_OpenBabel__DoubleType’
delete,_p_OpenBabel__FastSearch: no visible global function definition
  for ‘delete_OpenBabel__FastSearch’
delete,_p_OpenBabel__FastSearchIndexer: no visible global function
  definition for ‘delete_OpenBabel__FastSearchIndexer’
delete,_p_OpenBabel__FptIndexHeader: no visible global function
  definition for ‘delete_OpenBabel__FptIndexHeader’
delete,_p_OpenBabel__LineSearchType: no visible global function
  definition for ‘delete_OpenBabel__LineSearchType’
delete,_p_OpenBabel__OBAngle: no visible global function definition for
  ‘delete_OpenBabel__OBAngle’
delete,_p_OpenBabel__OBAngleData: no visible global function definition
  for ‘delete_OpenBabel__OBAngleData’
delete,_p_OpenBabel__OBAromaticTyper: no visible global function
  definition for ‘delete_OpenBabel__OBAromaticTyper’
delete,_p_OpenBabel__OBAtom: no visible global function definition for
  ‘delete_OpenBabel__OBAtom’
delete,_p_OpenBabel__OBAtomAtomIter: no visible global function
  definition for ‘delete_OpenBabel__OBAtomAtomIter’
delete,_p_OpenBabel__OBAtomBondIter: no visible global function
  definition for ‘delete_OpenBabel__OBAtomBondIter’
delete,_p_OpenBabel__OBAtomClassData: no visible global function
  definition for ‘delete_OpenBabel__OBAtomClassData’
delete,_p_OpenBabel__OBAtomTyper: no visible global function definition
  for ‘delete_OpenBabel__OBAtomTyper’
delete,_p_OpenBabel__OBBase: no visible global function definition for
  ‘delete_OpenBabel__OBBase’
delete,_p_OpenBabel__OBBitVec: no visible global function definition
  for ‘delete_OpenBabel__OBBitVec’
delete,_p_OpenBabel__OBBond: no visible global function definition for
  ‘delete_OpenBabel__OBBond’
delete,_p_OpenBabel__OBBuilder: no visible global function definition
  for ‘delete_OpenBabel__OBBuilder’
delete,_p_OpenBabel__OBChainsParser: no visible global function
  definition for ‘delete_OpenBabel__OBChainsParser’
delete,_p_OpenBabel__OBChiralData: no visible global function
  definition for ‘delete_OpenBabel__OBChiralData’
delete,_p_OpenBabel__OBCommentData: no visible global function
  definition for ‘delete_OpenBabel__OBCommentData’
delete,_p_OpenBabel__OBConformerData: no visible global function
  definition for ‘delete_OpenBabel__OBConformerData’
delete,_p_OpenBabel__OBConversion: no visible global function
  definition for ‘delete_OpenBabel__OBConversion’
delete,_p_OpenBabel__OBDOSData: no visible global function definition
  for ‘delete_OpenBabel__OBDOSData’
delete,_p_OpenBabel__OBDescriptor: no visible global function
  definition for ‘delete_OpenBabel__OBDescriptor’
delete,_p_OpenBabel__OBElectronicTransitionData: no visible global
  function definition for
  ‘delete_OpenBabel__OBElectronicTransitionData’
delete,_p_OpenBabel__OBElement: no visible global function definition
  for ‘delete_OpenBabel__OBElement’
delete,_p_OpenBabel__OBElementTable: no visible global function
  definition for ‘delete_OpenBabel__OBElementTable’
delete,_p_OpenBabel__OBError: no visible global function definition for
  ‘delete_OpenBabel__OBError’
delete,_p_OpenBabel__OBExternalBond: no visible global function
  definition for ‘delete_OpenBabel__OBExternalBond’
delete,_p_OpenBabel__OBExternalBondData: no visible global function
  definition for ‘delete_OpenBabel__OBExternalBondData’
delete,_p_OpenBabel__OBFFCalculation2: no visible global function
  definition for ‘delete_OpenBabel__OBFFCalculation2’
delete,_p_OpenBabel__OBFFCalculation3: no visible global function
  definition for ‘delete_OpenBabel__OBFFCalculation3’
delete,_p_OpenBabel__OBFFCalculation4: no visible global function
  definition for ‘delete_OpenBabel__OBFFCalculation4’
delete,_p_OpenBabel__OBFFConstraint: no visible global function
  definition for ‘delete_OpenBabel__OBFFConstraint’
delete,_p_OpenBabel__OBFFConstraints: no visible global function
  definition for ‘delete_OpenBabel__OBFFConstraints’
delete,_p_OpenBabel__OBFFParameter: no visible global function
  definition for ‘delete_OpenBabel__OBFFParameter’
delete,_p_OpenBabel__OBFingerprint: no visible global function
  definition for ‘delete_OpenBabel__OBFingerprint’
delete,_p_OpenBabel__OBForceField: no visible global function
  definition for ‘delete_OpenBabel__OBForceField’
delete,_p_OpenBabel__OBFormat: no visible global function definition
  for ‘delete_OpenBabel__OBFormat’
delete,_p_OpenBabel__OBGenericData: no visible global function
  definition for ‘delete_OpenBabel__OBGenericData’
delete,_p_OpenBabel__OBGlobalDataBase: no visible global function
  definition for ‘delete_OpenBabel__OBGlobalDataBase’
delete,_p_OpenBabel__OBGridData: no visible global function definition
  for ‘delete_OpenBabel__OBGridData’
delete,_p_OpenBabel__OBInternalCoord: no visible global function
  definition for ‘delete_OpenBabel__OBInternalCoord’
delete,_p_OpenBabel__OBIsotopeTable: no visible global function
  definition for ‘delete_OpenBabel__OBIsotopeTable’
delete,_p_OpenBabel__OBMatrixData: no visible global function
  definition for ‘delete_OpenBabel__OBMatrixData’
delete,_p_OpenBabel__OBMessageHandler: no visible global function
  definition for ‘delete_OpenBabel__OBMessageHandler’
delete,_p_OpenBabel__OBMol: no visible global function definition for
  ‘delete_OpenBabel__OBMol’
delete,_p_OpenBabel__OBMolAngleIter: no visible global function
  definition for ‘delete_OpenBabel__OBMolAngleIter’
delete,_p_OpenBabel__OBMolAtomBFSIter: no visible global function
  definition for ‘delete_OpenBabel__OBMolAtomBFSIter’
delete,_p_OpenBabel__OBMolAtomDFSIter: no visible global function
  definition for ‘delete_OpenBabel__OBMolAtomDFSIter’
delete,_p_OpenBabel__OBMolAtomIter: no visible global function
  definition for ‘delete_OpenBabel__OBMolAtomIter’
delete,_p_OpenBabel__OBMolBondBFSIter: no visible global function
  definition for ‘delete_OpenBabel__OBMolBondBFSIter’
delete,_p_OpenBabel__OBMolBondIter: no visible global function
  definition for ‘delete_OpenBabel__OBMolBondIter’
delete,_p_OpenBabel__OBMolPairIter: no visible global function
  definition for ‘delete_OpenBabel__OBMolPairIter’
delete,_p_OpenBabel__OBMolRingIter: no visible global function
  definition for ‘delete_OpenBabel__OBMolRingIter’
delete,_p_OpenBabel__OBMolTorsionIter: no visible global function
  definition for ‘delete_OpenBabel__OBMolTorsionIter’
delete,_p_OpenBabel__OBOp: no visible global function definition for
  ‘delete_OpenBabel__OBOp’
delete,_p_OpenBabel__OBOrbital: no visible global function definition
  for ‘delete_OpenBabel__OBOrbital’
delete,_p_OpenBabel__OBOrbitalData: no visible global function
  definition for ‘delete_OpenBabel__OBOrbitalData’
delete,_p_OpenBabel__OBPairData: no visible global function definition
  for ‘delete_OpenBabel__OBPairData’
delete,_p_OpenBabel__OBPlugin: no visible global function definition
  for ‘delete_OpenBabel__OBPlugin’
delete,_p_OpenBabel__OBRTree: no visible global function definition for
  ‘delete_OpenBabel__OBRTree’
delete,_p_OpenBabel__OBRandom: no visible global function definition
  for ‘delete_OpenBabel__OBRandom’
delete,_p_OpenBabel__OBResidue: no visible global function definition
  for ‘delete_OpenBabel__OBResidue’
delete,_p_OpenBabel__OBResidueAtomIter: no visible global function
  definition for ‘delete_OpenBabel__OBResidueAtomIter’
delete,_p_OpenBabel__OBResidueData: no visible global function
  definition for ‘delete_OpenBabel__OBResidueData’
delete,_p_OpenBabel__OBResidueIter: no visible global function
  definition for ‘delete_OpenBabel__OBResidueIter’
delete,_p_OpenBabel__OBRing: no visible global function definition for
  ‘delete_OpenBabel__OBRing’
delete,_p_OpenBabel__OBRingData: no visible global function definition
  for ‘delete_OpenBabel__OBRingData’
delete,_p_OpenBabel__OBRingSearch: no visible global function
  definition for ‘delete_OpenBabel__OBRingSearch’
delete,_p_OpenBabel__OBRingTyper: no visible global function definition
  for ‘delete_OpenBabel__OBRingTyper’
delete,_p_OpenBabel__OBRotationData: no visible global function
  definition for ‘delete_OpenBabel__OBRotationData’
delete,_p_OpenBabel__OBSSMatch: no visible global function definition
  for ‘delete_OpenBabel__OBSSMatch’
delete,_p_OpenBabel__OBSerialNums: no visible global function
  definition for ‘delete_OpenBabel__OBSerialNums’
delete,_p_OpenBabel__OBSetData: no visible global function definition
  for ‘delete_OpenBabel__OBSetData’
delete,_p_OpenBabel__OBSmartsMatcher: no visible global function
  definition for ‘delete_OpenBabel__OBSmartsMatcher’
delete,_p_OpenBabel__OBSmartsPattern: no visible global function
  definition for ‘delete_OpenBabel__OBSmartsPattern’
delete,_p_OpenBabel__OBSqrtTbl: no visible global function definition
  for ‘delete_OpenBabel__OBSqrtTbl’
delete,_p_OpenBabel__OBStopwatch: no visible global function definition
  for ‘delete_OpenBabel__OBStopwatch’
delete,_p_OpenBabel__OBSymmetryData: no visible global function
  definition for ‘delete_OpenBabel__OBSymmetryData’
delete,_p_OpenBabel__OBTorsion: no visible global function definition
  for ‘delete_OpenBabel__OBTorsion’
delete,_p_OpenBabel__OBTorsionData: no visible global function
  definition for ‘delete_OpenBabel__OBTorsionData’
delete,_p_OpenBabel__OBTypeTable: no visible global function definition
  for ‘delete_OpenBabel__OBTypeTable’
delete,_p_OpenBabel__OBUnitCell: no visible global function definition
  for ‘delete_OpenBabel__OBUnitCell’
delete,_p_OpenBabel__OBVectorData: no visible global function
  definition for ‘delete_OpenBabel__OBVectorData’
delete,_p_OpenBabel__OBVibrationData: no visible global function
  definition for ‘delete_OpenBabel__OBVibrationData’
delete,_p_OpenBabel__OBVirtualBond: no visible global function
  definition for ‘delete_OpenBabel__OBVirtualBond’
delete,_p_OpenBabel__SpaceGroup: no visible global function definition
  for ‘delete_OpenBabel__SpaceGroup’
delete,_p_OpenBabel__matrix3x3: no visible global function definition
  for ‘delete_OpenBabel__matrix3x3’
delete,_p_OpenBabel__obLogBuf: no visible global function definition
  for ‘delete_OpenBabel__obLogBuf’
delete,_p_OpenBabel__transform3d: no visible global function definition
  for ‘delete_OpenBabel__transform3d’
delete,_p_OpenBabel__vector3: no visible global function definition for
  ‘delete_OpenBabel__vector3’
delete,_p_std__binary_functionT_char_const_p_char_const_p_bool_t: no
  visible global function definition for
  ‘delete_std__binary_functionT_char_const_p_char_const_p_bool_t’
delete,_p_std__pairT_unsigned_int_unsigned_int_t: no visible global
  function definition for
  ‘delete_std__pairT_unsigned_int_unsigned_int_t’
delete,_p_std__stringbuf: no visible global function definition for
  ‘delete_std__stringbuf’
delete,_p_std__vectorT_OpenBabel__OBBond_std__allocatorT_OpenBabel__OBBond_t_t:
  no visible global function definition for
  ‘delete_std__vectorT_OpenBabel__OBBond_std__allocatorT_OpenBabel__OBBond_t_t’
delete,_p_std__vectorT_OpenBabel__OBGenericData_p_std__allocatorT_OpenBabel__OBGenericData_p_t_t:
  no visible global function definition for
  ‘delete_std__vectorT_OpenBabel__OBGenericData_p_std__allocatorT_OpenBabel__OBGenericData_p_t_t’
delete,_p_std__vectorT_OpenBabel__OBInternalCoord_p_std__allocatorT_OpenBabel__OBInternalCoord_p_t_t:
  no visible global function definition for
  ‘delete_std__vectorT_OpenBabel__OBInternalCoord_p_std__allocatorT_OpenBabel__OBInternalCoord_p_t_t’
delete,_p_std__vectorT_OpenBabel__OBMol_std__allocatorT_OpenBabel__OBMol_t_t:
  no visible global function definition for
  ‘delete_std__vectorT_OpenBabel__OBMol_std__allocatorT_OpenBabel__OBMol_t_t’
delete,_p_std__vectorT_OpenBabel__OBResidue_std__allocatorT_OpenBabel__OBResidue_t_t:
  no visible global function definition for
  ‘delete_std__vectorT_OpenBabel__OBResidue_std__allocatorT_OpenBabel__OBResidue_t_t’
delete,_p_std__vectorT_OpenBabel__OBRing_p_std__allocatorT_OpenBabel__OBRing_p_t_t:
  no visible global function definition for
  ‘delete_std__vectorT_OpenBabel__OBRing_p_std__allocatorT_OpenBabel__OBRing_p_t_t’
delete,_p_std__vectorT_OpenBabel__OBRing_std__allocatorT_OpenBabel__OBRing_t_t:
  no visible global function definition for
  ‘delete_std__vectorT_OpenBabel__OBRing_std__allocatorT_OpenBabel__OBRing_t_t’
delete,_p_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t:
  no visible global function definition for
  ‘delete_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t’
delete,_p_std__vectorT_double_std__allocatorT_double_t_t: no visible
  global function definition for
  ‘delete_std__vectorT_double_std__allocatorT_double_t_t’
delete,_p_std__vectorT_int_std__allocatorT_int_t_t: no visible global
  function definition for
  ‘delete_std__vectorT_int_std__allocatorT_int_t_t’
delete,_p_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t:
  no visible global function definition for
  ‘delete_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t’
delete,_p_std__vectorT_std__string_std__allocatorT_std__string_t_t: no
  visible global function definition for
  ‘delete_std__vectorT_std__string_std__allocatorT_std__string_t_t’
delete,_p_std__vectorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_std__allocatorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_t_t:
  no visible global function definition for
  ‘delete_std__vectorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_std__allocatorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_t_t’
delete,_p_std__vectorT_std__vectorT_int_std__allocatorT_int_t_t_std__allocatorT_std__vectorT_int_std__allocatorT_int_t_t_t_t:
  no visible global function definition for
  ‘delete_std__vectorT_std__vectorT_int_std__allocatorT_int_t_t_std__allocatorT_std__vectorT_int_std__allocatorT_int_t_t_t_t’
delete,_p_std__vectorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_std__allocatorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_t_t:
  no visible global function definition for
  ‘delete_std__vectorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_std__allocatorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_t_t’
delete,_p_std__vectorT_unsigned_int_std__allocatorT_unsigned_int_t_t:
  no visible global function definition for
  ‘delete_std__vectorT_unsigned_int_std__allocatorT_unsigned_int_t_t’
* checking Rd files ... NOTE
prepare_Rd: canonicalNumbering_OB.Rd:30-32: Dropping empty section \note
prepare_Rd: forEachMol.Rd:48-50: Dropping empty section \seealso
* 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 ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
  -stdlib=libstdc++
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
  src/Makevars.in
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘ChemmineOB/libs/ChemmineOB.so’:
  Found ‘__ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘ChemmineOB.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [5s/5s]
 [5s/5s] 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 WARNINGs, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChemmineOB.Rcheck/00check.log’
for details.

* installing *source* package ‘ChemmineOB’ ...
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENBABEL... yes
checking for OPENBABEL... yes
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -stdlib=libstdc++ -I/usr/local/include/openbabel-2.0    -I/usr/include/eigen3  -DUSE_BOOST -fPIC  -Wall -mtune=core2 -g -O2  -c ChemmineOB.cpp -o ChemmineOB.o
In file included from ChemmineOB.cpp:1476:
/usr/local/include/openbabel-2.0/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual]
    double GetValue(int i, int j, int k) const;
           ^
/usr/local/include/openbabel-2.0/openbabel/base.h:229:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3)
    virtual const std::string &GetValue()  const
                               ^
In file included from ChemmineOB.cpp:1476:
/usr/local/include/openbabel-2.0/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual]
    double GetValue (vector3 pos) const;
           ^
/usr/local/include/openbabel-2.0/openbabel/base.h:229:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1)
    virtual const std::string &GetValue()  const
                               ^
In file included from ChemmineOB.cpp:1493:
In file included from /usr/local/include/openbabel-2.0/openbabel/forcefield.h:32:
/usr/local/include/openbabel-2.0/openbabel/grid.h:123:10: warning: 'OpenBabel::OBFloatGrid::Init' hides overloaded virtual function [-Woverloaded-virtual]
    void Init(OBMol &box,double spacing, double pad=0.0);
         ^
/usr/local/include/openbabel-2.0/openbabel/grid.h:55:18: note: hidden overloaded virtual function 'OpenBabel::OBGrid::Init' declared here: different number of parameters (1 vs 3)
    virtual void Init(OBMol &box);
                 ^
ChemmineOB.cpp:31483:14: warning: explicitly assigning a variable of type 'void *' to itself [-Wself-assign]
  clientdata = clientdata;
  ˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -stdlib=libstdc++ -I/usr/local/include/openbabel-2.0    -I/usr/include/eigen3  -DUSE_BOOST -fPIC  -Wall -mtune=core2 -g -O2  -c canonical.cpp -o canonical.o
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 ChemmineOB.so ChemmineOB.o canonical.o -stdlib=libstdc++ -L/usr/local/lib -lopenbabel -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/ChemmineOB.Rcheck/ChemmineOB/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘ChemmineOB’
in method for ‘copyToR’ with signature ‘"_p_std::pair<(unsigned int,unsigned int)>"’: no definition for class “_p_std::pair<(unsigned int,unsigned int)>”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::DoubleType"’: no definition for class “_p_OpenBabel::DoubleType”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::CharPtrLess"’: no definition for class “_p_OpenBabel::CharPtrLess”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::FptIndexHeader"’: no definition for class “_p_OpenBabel::FptIndexHeader”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::LineSearchType"’: no definition for class “_p_OpenBabel::LineSearchType”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChemmineOB)

name	user	system	elapsed
canonicalNumbering_OB	1.522	0.098	2.615
convertFormat	0.006	0.001	0.019
convertFormatFile	0.001	0.000	0.000
exactMass_OB	0.007	0.001	0.020
fingerprint_OB	0.006	0.001	0.018
forEachMol	0.002	0.001	0.003
prop_OB	0.024	0.003	0.118
smartsSearch_OB	0.002	0.000	0.003