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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ChemmineOB.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ChemmineOB_1.44.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ChemmineOB.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ChemmineOB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineOB’ version ‘1.44.0’
* 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 ... WARNING
Found the following significant warnings:
  /usr/include/openbabel3/openbabel/plugin.h:41:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  ChemmineOB.cpp:13728:45: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  ChemmineOB.cpp:13730:18: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  ChemmineOB.cpp:13730:79: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  ChemmineOB.cpp:13734:8: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  ChemmineOB.cpp:13734:72: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  ChemmineOB.cpp:13739:34: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  ChemmineOB.cpp:39656:27: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ChemmineOB.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... NOTE
  installed size is 23.3Mb
  sub-directories of 1Mb or more:
    R                3.8Mb
    libs            17.3Mb
    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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... 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 ... WARNING
Foreign function calls without 'PACKAGE' argument:
  .Call("R_SWIG_R_pushCallbackFunctionData", ...)
  .Call("R_SWIG_debug_getCallbackFunctionData", ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
cerr: no visible global function definition for ‘cerr_set’
cin: no visible global function definition for ‘cin_set’
clog: no visible global function definition for ‘clog_set’
cout: no visible global function definition for ‘cout_set’
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__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__OBAlign: no visible global function definition for
  ‘delete_OpenBabel__OBAlign’
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__OBAtomHOF: no visible global function definition
  for ‘delete_OpenBabel__OBAtomHOF’
delete,_p_OpenBabel__OBAtomTyper: no visible global function definition
  for ‘delete_OpenBabel__OBAtomTyper’
delete,_p_OpenBabel__OBAtomicHeatOfFormationTable: no visible global
  function definition for
  ‘delete_OpenBabel__OBAtomicHeatOfFormationTable’
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__OBChargeModel: no visible global function
  definition for ‘delete_OpenBabel__OBChargeModel’
delete,_p_OpenBabel__OBCisTransConfig: no visible global function
  definition for ‘delete_OpenBabel__OBCisTransConfig’
delete,_p_OpenBabel__OBCisTransStereo: no visible global function
  definition for ‘delete_OpenBabel__OBCisTransStereo’
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__OBConformerFilter: no visible global function
  definition for ‘delete_OpenBabel__OBConformerFilter’
delete,_p_OpenBabel__OBConformerFilters: no visible global function
  definition for ‘delete_OpenBabel__OBConformerFilters’
delete,_p_OpenBabel__OBConformerScore: no visible global function
  definition for ‘delete_OpenBabel__OBConformerScore’
delete,_p_OpenBabel__OBConformerSearch: no visible global function
  definition for ‘delete_OpenBabel__OBConformerSearch’
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__OBEnergyConformerScore: no visible global function
  definition for ‘delete_OpenBabel__OBEnergyConformerScore’
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__OBFreeGrid: no visible global function definition
  for ‘delete_OpenBabel__OBFreeGrid’
delete,_p_OpenBabel__OBFreeGridPoint: no visible global function
  definition for ‘delete_OpenBabel__OBFreeGridPoint’
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__OBGraphSym: no visible global function definition
  for ‘delete_OpenBabel__OBGraphSym’
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__OBIsomorphismMapper: no visible global function
  definition for ‘delete_OpenBabel__OBIsomorphismMapper’
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__OBMinimizingEnergyConformerScore: no visible
  global function definition for
  ‘delete_OpenBabel__OBMinimizingEnergyConformerScore’
delete,_p_OpenBabel__OBMinimizingRMSDConformerScore: no visible global
  function definition for
  ‘delete_OpenBabel__OBMinimizingRMSDConformerScore’
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__OBPcharge: no visible global function definition
  for ‘delete_OpenBabel__OBPcharge’
delete,_p_OpenBabel__OBPlugin: no visible global function definition
  for ‘delete_OpenBabel__OBPlugin’
delete,_p_OpenBabel__OBQuery: no visible global function definition for
  ‘delete_OpenBabel__OBQuery’
delete,_p_OpenBabel__OBQueryAtom: no visible global function definition
  for ‘delete_OpenBabel__OBQueryAtom’
delete,_p_OpenBabel__OBQueryBond: no visible global function definition
  for ‘delete_OpenBabel__OBQueryBond’
delete,_p_OpenBabel__OBRMSDConformerScore: no visible global function
  definition for ‘delete_OpenBabel__OBRMSDConformerScore’
delete,_p_OpenBabel__OBRTree: no visible global function definition for
  ‘delete_OpenBabel__OBRTree’
delete,_p_OpenBabel__OBReaction: no visible global function definition
  for ‘delete_OpenBabel__OBReaction’
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__OBRotamerList: no visible global function
  definition for ‘delete_OpenBabel__OBRotamerList’
delete,_p_OpenBabel__OBRotationData: no visible global function
  definition for ‘delete_OpenBabel__OBRotationData’
delete,_p_OpenBabel__OBRotor: no visible global function definition for
  ‘delete_OpenBabel__OBRotor’
delete,_p_OpenBabel__OBRotorKeys: no visible global function definition
  for ‘delete_OpenBabel__OBRotorKeys’
delete,_p_OpenBabel__OBRotorList: no visible global function definition
  for ‘delete_OpenBabel__OBRotorList’
delete,_p_OpenBabel__OBRotorRule: no visible global function definition
  for ‘delete_OpenBabel__OBRotorRule’
delete,_p_OpenBabel__OBRotorRules: no visible global function
  definition for ‘delete_OpenBabel__OBRotorRules’
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__OBSpectrophore: no visible global function
  definition for ‘delete_OpenBabel__OBSpectrophore’
delete,_p_OpenBabel__OBSqrtTbl: no visible global function definition
  for ‘delete_OpenBabel__OBSqrtTbl’
delete,_p_OpenBabel__OBSquarePlanarConfig: no visible global function
  definition for ‘delete_OpenBabel__OBSquarePlanarConfig’
delete,_p_OpenBabel__OBSquarePlanarStereo: no visible global function
  definition for ‘delete_OpenBabel__OBSquarePlanarStereo’
delete,_p_OpenBabel__OBStereo: no visible global function definition
  for ‘delete_OpenBabel__OBStereo’
delete,_p_OpenBabel__OBStereoBase: no visible global function
  definition for ‘delete_OpenBabel__OBStereoBase’
delete,_p_OpenBabel__OBStereoFacade: no visible global function
  definition for ‘delete_OpenBabel__OBStereoFacade’
delete,_p_OpenBabel__OBStereoUnit: no visible global function
  definition for ‘delete_OpenBabel__OBStereoUnit’
delete,_p_OpenBabel__OBStericConformerFilter: no visible global
  function definition for ‘delete_OpenBabel__OBStericConformerFilter’
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__OBTetraNonPlanarStereo: no visible global function
  definition for ‘delete_OpenBabel__OBTetraNonPlanarStereo’
delete,_p_OpenBabel__OBTetraPlanarStereo: no visible global function
  definition for ‘delete_OpenBabel__OBTetraPlanarStereo’
delete,_p_OpenBabel__OBTetrahedralConfig: no visible global function
  definition for ‘delete_OpenBabel__OBTetrahedralConfig’
delete,_p_OpenBabel__OBTetrahedralStereo: no visible global function
  definition for ‘delete_OpenBabel__OBTetrahedralStereo’
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__rotor_digit: no visible global function definition
  for ‘delete_OpenBabel__rotor_digit’
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__basic_iosT_char_std__char_traitsT_char_t_t: no visible
  global function definition for
  ‘delete_std__basic_iosT_char_std__char_traitsT_char_t_t’
delete,_p_std__basic_iostreamT_char_std__char_traitsT_char_t_t: no
  visible global function definition for
  ‘delete_std__basic_iostreamT_char_std__char_traitsT_char_t_t’
delete,_p_std__basic_istreamT_char_std__char_traitsT_char_t_t: no
  visible global function definition for
  ‘delete_std__basic_istreamT_char_std__char_traitsT_char_t_t’
delete,_p_std__basic_ostreamT_char_std__char_traitsT_char_t_t: no
  visible global function definition for
  ‘delete_std__basic_ostreamT_char_std__char_traitsT_char_t_t’
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__ios_base: no visible global function definition for
  ‘delete_std__ios_base’
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’
Undefined global functions or variables:
  cerr_set cin_set clog_set cout_set delete_OpenBabel__AliasData
  delete_OpenBabel__CharPtrLess delete_OpenBabel__FastSearch
  delete_OpenBabel__FastSearchIndexer delete_OpenBabel__FptIndexHeader
  delete_OpenBabel__LineSearchType delete_OpenBabel__OBAlign
  delete_OpenBabel__OBAngle delete_OpenBabel__OBAngleData
  delete_OpenBabel__OBAromaticTyper delete_OpenBabel__OBAtom
  delete_OpenBabel__OBAtomAtomIter delete_OpenBabel__OBAtomBondIter
  delete_OpenBabel__OBAtomHOF delete_OpenBabel__OBAtomTyper
  delete_OpenBabel__OBAtomicHeatOfFormationTable
  delete_OpenBabel__OBBase delete_OpenBabel__OBBitVec
  delete_OpenBabel__OBBond delete_OpenBabel__OBBuilder
  delete_OpenBabel__OBChainsParser delete_OpenBabel__OBChargeModel
  delete_OpenBabel__OBCisTransConfig delete_OpenBabel__OBCisTransStereo
  delete_OpenBabel__OBCommentData delete_OpenBabel__OBConformerData
  delete_OpenBabel__OBConformerFilter
  delete_OpenBabel__OBConformerFilters
  delete_OpenBabel__OBConformerScore
  delete_OpenBabel__OBConformerSearch delete_OpenBabel__OBConversion
  delete_OpenBabel__OBDOSData delete_OpenBabel__OBDescriptor
  delete_OpenBabel__OBElectronicTransitionData
  delete_OpenBabel__OBEnergyConformerScore delete_OpenBabel__OBError
  delete_OpenBabel__OBExternalBond delete_OpenBabel__OBExternalBondData
  delete_OpenBabel__OBFFCalculation2 delete_OpenBabel__OBFFCalculation3
  delete_OpenBabel__OBFFCalculation4 delete_OpenBabel__OBFFConstraint
  delete_OpenBabel__OBFFConstraints delete_OpenBabel__OBFFParameter
  delete_OpenBabel__OBFingerprint delete_OpenBabel__OBForceField
  delete_OpenBabel__OBFormat delete_OpenBabel__OBFreeGrid
  delete_OpenBabel__OBFreeGridPoint delete_OpenBabel__OBGenericData
  delete_OpenBabel__OBGlobalDataBase delete_OpenBabel__OBGraphSym
  delete_OpenBabel__OBGridData delete_OpenBabel__OBInternalCoord
  delete_OpenBabel__OBIsomorphismMapper delete_OpenBabel__OBMatrixData
  delete_OpenBabel__OBMessageHandler
  delete_OpenBabel__OBMinimizingEnergyConformerScore
  delete_OpenBabel__OBMinimizingRMSDConformerScore
  delete_OpenBabel__OBMol delete_OpenBabel__OBMolAngleIter
  delete_OpenBabel__OBMolAtomBFSIter delete_OpenBabel__OBMolAtomDFSIter
  delete_OpenBabel__OBMolAtomIter delete_OpenBabel__OBMolBondBFSIter
  delete_OpenBabel__OBMolBondIter delete_OpenBabel__OBMolPairIter
  delete_OpenBabel__OBMolRingIter delete_OpenBabel__OBMolTorsionIter
  delete_OpenBabel__OBOp delete_OpenBabel__OBOrbital
  delete_OpenBabel__OBOrbitalData delete_OpenBabel__OBPairData
  delete_OpenBabel__OBPcharge delete_OpenBabel__OBPlugin
  delete_OpenBabel__OBQuery delete_OpenBabel__OBQueryAtom
  delete_OpenBabel__OBQueryBond delete_OpenBabel__OBRMSDConformerScore
  delete_OpenBabel__OBRTree delete_OpenBabel__OBReaction
  delete_OpenBabel__OBResidue delete_OpenBabel__OBResidueAtomIter
  delete_OpenBabel__OBResidueData delete_OpenBabel__OBResidueIter
  delete_OpenBabel__OBRing delete_OpenBabel__OBRingData
  delete_OpenBabel__OBRingSearch delete_OpenBabel__OBRingTyper
  delete_OpenBabel__OBRotamerList delete_OpenBabel__OBRotationData
  delete_OpenBabel__OBRotor delete_OpenBabel__OBRotorKeys
  delete_OpenBabel__OBRotorList delete_OpenBabel__OBRotorRule
  delete_OpenBabel__OBRotorRules delete_OpenBabel__OBSSMatch
  delete_OpenBabel__OBSerialNums delete_OpenBabel__OBSetData
  delete_OpenBabel__OBSmartsMatcher delete_OpenBabel__OBSmartsPattern
  delete_OpenBabel__OBSpectrophore delete_OpenBabel__OBSqrtTbl
  delete_OpenBabel__OBSquarePlanarConfig
  delete_OpenBabel__OBSquarePlanarStereo delete_OpenBabel__OBStereo
  delete_OpenBabel__OBStereoBase delete_OpenBabel__OBStereoFacade
  delete_OpenBabel__OBStereoUnit
  delete_OpenBabel__OBStericConformerFilter
  delete_OpenBabel__OBStopwatch delete_OpenBabel__OBSymmetryData
  delete_OpenBabel__OBTetraNonPlanarStereo
  delete_OpenBabel__OBTetraPlanarStereo
  delete_OpenBabel__OBTetrahedralConfig
  delete_OpenBabel__OBTetrahedralStereo delete_OpenBabel__OBTorsion
  delete_OpenBabel__OBTorsionData delete_OpenBabel__OBTypeTable
  delete_OpenBabel__OBUnitCell delete_OpenBabel__OBVectorData
  delete_OpenBabel__OBVibrationData delete_OpenBabel__OBVirtualBond
  delete_OpenBabel__SpaceGroup delete_OpenBabel__matrix3x3
  delete_OpenBabel__obLogBuf delete_OpenBabel__rotor_digit
  delete_OpenBabel__transform3d delete_OpenBabel__vector3
  delete_std__basic_iosT_char_std__char_traitsT_char_t_t
  delete_std__basic_iostreamT_char_std__char_traitsT_char_t_t
  delete_std__basic_istreamT_char_std__char_traitsT_char_t_t
  delete_std__basic_ostreamT_char_std__char_traitsT_char_t_t
  delete_std__binary_functionT_char_const_p_char_const_p_bool_t
  delete_std__ios_base delete_std__pairT_unsigned_int_unsigned_int_t
  delete_std__stringbuf
  delete_std__vectorT_OpenBabel__OBBond_std__allocatorT_OpenBabel__OBBond_t_t
  delete_std__vectorT_OpenBabel__OBGenericData_p_std__allocatorT_OpenBabel__OBGenericData_p_t_t
  delete_std__vectorT_OpenBabel__OBInternalCoord_p_std__allocatorT_OpenBabel__OBInternalCoord_p_t_t
  delete_std__vectorT_OpenBabel__OBMol_std__allocatorT_OpenBabel__OBMol_t_t
  delete_std__vectorT_OpenBabel__OBResidue_std__allocatorT_OpenBabel__OBResidue_t_t
  delete_std__vectorT_OpenBabel__OBRing_p_std__allocatorT_OpenBabel__OBRing_p_t_t
  delete_std__vectorT_OpenBabel__OBRing_std__allocatorT_OpenBabel__OBRing_t_t
  delete_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t
  delete_std__vectorT_double_std__allocatorT_double_t_t
  delete_std__vectorT_int_std__allocatorT_int_t_t
  delete_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t
  delete_std__vectorT_std__string_std__allocatorT_std__string_t_t
  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_std__vectorT_std__vectorT_int_std__allocatorT_int_t_t_std__allocatorT_std__vectorT_int_std__allocatorT_int_t_t_t_t
  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_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 ... WARNING
Undocumented S4 methods:
  generic '$' and siglist '_p_OpenBabel__OBAlign'
  generic '$' and siglist '_p_OpenBabel__OBAtomHOF'
  generic '$' and siglist '_p_OpenBabel__OBAtomicHeatOfFormationTable'
  generic '$' and siglist '_p_OpenBabel__OBChargeModel'
  generic '$' and siglist '_p_OpenBabel__OBCisTransConfig'
  generic '$' and siglist '_p_OpenBabel__OBCisTransStereo'
  generic '$' and siglist '_p_OpenBabel__OBConformerFilter'
  generic '$' and siglist '_p_OpenBabel__OBConformerScore'
  generic '$' and siglist '_p_OpenBabel__OBConformerSearch'
  generic '$' and siglist '_p_OpenBabel__OBEnergyConformerScore'
  generic '$' and siglist '_p_OpenBabel__OBFreeGrid'
  generic '$' and siglist '_p_OpenBabel__OBFreeGridPoint'
  generic '$' and siglist '_p_OpenBabel__OBGraphSym'
  generic '$' and siglist '_p_OpenBabel__OBIsomorphismMapper'
  generic '$' and siglist
    '_p_OpenBabel__OBMinimizingEnergyConformerScore'
  generic '$' and siglist '_p_OpenBabel__OBPcharge'
  generic '$' and siglist '_p_OpenBabel__OBQuery'
  generic '$' and siglist '_p_OpenBabel__OBQueryAtom'
  generic '$' and siglist '_p_OpenBabel__OBQueryBond'
  generic '$' and siglist '_p_OpenBabel__OBReaction'
  generic '$' and siglist '_p_OpenBabel__OBRotamerList'
  generic '$' and siglist '_p_OpenBabel__OBRotor'
  generic '$' and siglist '_p_OpenBabel__OBRotorKeys'
  generic '$' and siglist '_p_OpenBabel__OBRotorList'
  generic '$' and siglist '_p_OpenBabel__OBRotorRule'
  generic '$' and siglist '_p_OpenBabel__OBRotorRules'
  generic '$' and siglist '_p_OpenBabel__OBSpectrophore'
  generic '$' and siglist '_p_OpenBabel__OBSquarePlanarConfig'
  generic '$' and siglist '_p_OpenBabel__OBSquarePlanarStereo'
  generic '$' and siglist '_p_OpenBabel__OBStereoBase'
  generic '$' and siglist '_p_OpenBabel__OBStereoFacade'
  generic '$' and siglist '_p_OpenBabel__OBStereoUnit'
  generic '$' and siglist '_p_OpenBabel__OBTetrahedralConfig'
  generic '$' and siglist '_p_OpenBabel__OBTetrahedralStereo'
  generic '$' and siglist '_p_OpenBabel__rotor_digit'
  generic '$' and siglist
    '_p_std__basic_iosT_char_std__char_traitsT_char_t_t'
  generic '$' and siglist
    '_p_std__basic_istreamT_char_std__char_traitsT_char_t_t'
  generic '$' and siglist
    '_p_std__basic_ostreamT_char_std__char_traitsT_char_t_t'
  generic '$' and siglist '_p_std__ios_base'
  generic '$<-' and siglist '_p_OpenBabel__OBCisTransConfig'
  generic '$<-' and siglist '_p_OpenBabel__OBSquarePlanarConfig'
  generic '$<-' and siglist '_p_OpenBabel__OBStereoUnit'
  generic '$<-' and siglist '_p_OpenBabel__OBTetrahedralConfig'
  generic '[[<-' and siglist '_p_OpenBabel__OBCisTransConfig,character'
  generic '[[<-' and siglist
    '_p_OpenBabel__OBSquarePlanarConfig,character'
  generic '[[<-' and siglist '_p_OpenBabel__OBStereoUnit,character'
  generic '[[<-' and siglist
    '_p_OpenBabel__OBTetrahedralConfig,character'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/ChemmineOB/libs/ChemmineOB.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘abort’, possibly from ‘abort’ (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 nor [v]sprintf. 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 7 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ChemmineOB.Rcheck/00check.log’
for details.