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BioC 3.4: CHECK report for ChemmineOB on tokay1

This page was generated on 2017-04-15 16:18:08 -0400 (Sat, 15 Apr 2017).

Package 187/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineOB 1.12.0
Thomas Girke
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ChemmineOB
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChemmineOB
Version: 1.12.0
Command: rm -rf ChemmineOB.buildbin-libdir ChemmineOB.Rcheck && mkdir ChemmineOB.buildbin-libdir ChemmineOB.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChemmineOB.buildbin-libdir ChemmineOB_1.12.0.tar.gz >ChemmineOB.Rcheck\00install.out 2>&1 && cp ChemmineOB.Rcheck\00install.out ChemmineOB-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ChemmineOB.buildbin-libdir --install="check:ChemmineOB-install.out" --force-multiarch --no-vignettes --timings ChemmineOB_1.12.0.tar.gz
StartedAt: 2017-04-14 21:25:43 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:30:27 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 283.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ChemmineOB.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf ChemmineOB.buildbin-libdir ChemmineOB.Rcheck && mkdir ChemmineOB.buildbin-libdir ChemmineOB.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChemmineOB.buildbin-libdir ChemmineOB_1.12.0.tar.gz >ChemmineOB.Rcheck\00install.out 2>&1 && cp ChemmineOB.Rcheck\00install.out ChemmineOB-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ChemmineOB.buildbin-libdir --install="check:ChemmineOB-install.out" --force-multiarch --no-vignettes --timings ChemmineOB_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/ChemmineOB.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChemmineOB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChemmineOB' version '1.12.0'
* 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 whether package 'ChemmineOB' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 16.1Mb
  sub-directories of 1Mb or more:
    R                1.3Mb
    libs            12.6Mb
    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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
Undefined global functions or variables:
  RSWIG_createNewRef delete_OpenBabel__AliasData
  delete_OpenBabel__CharPtrLess delete_OpenBabel__DoubleType
  delete_OpenBabel__FastSearch delete_OpenBabel__FastSearchIndexer
  delete_OpenBabel__FptIndexHeader delete_OpenBabel__LineSearchType
  delete_OpenBabel__OBAngle delete_OpenBabel__OBAngleData
  delete_OpenBabel__OBAromaticTyper delete_OpenBabel__OBAtom
  delete_OpenBabel__OBAtomAtomIter delete_OpenBabel__OBAtomBondIter
  delete_OpenBabel__OBAtomClassData delete_OpenBabel__OBAtomTyper
  delete_OpenBabel__OBBase delete_OpenBabel__OBBitVec
  delete_OpenBabel__OBBond delete_OpenBabel__OBBuilder
  delete_OpenBabel__OBChainsParser delete_OpenBabel__OBChiralData
  delete_OpenBabel__OBCommentData delete_OpenBabel__OBConformerData
  delete_OpenBabel__OBConversion delete_OpenBabel__OBDOSData
  delete_OpenBabel__OBDescriptor
  delete_OpenBabel__OBElectronicTransitionData
  delete_OpenBabel__OBElement delete_OpenBabel__OBElementTable
  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__OBGenericData
  delete_OpenBabel__OBGlobalDataBase delete_OpenBabel__OBGridData
  delete_OpenBabel__OBInternalCoord delete_OpenBabel__OBIsotopeTable
  delete_OpenBabel__OBMatrixData delete_OpenBabel__OBMessageHandler
  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__OBPlugin delete_OpenBabel__OBRTree
  delete_OpenBabel__OBRandom 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__OBRotationData
  delete_OpenBabel__OBSSMatch delete_OpenBabel__OBSerialNums
  delete_OpenBabel__OBSetData delete_OpenBabel__OBSmartsMatcher
  delete_OpenBabel__OBSmartsPattern delete_OpenBabel__OBSqrtTbl
  delete_OpenBabel__OBStopwatch delete_OpenBabel__OBSymmetryData
  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__transform3d delete_OpenBabel__vector3
  delete_std__binary_functionT_char_const_p_char_const_p_bool_t
  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 ... 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 ... WARNING
Found the following file(s) containing GNU extensions:
  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
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.4-bioc/meat/ChemmineOB.buildbin-libdir/ChemmineOB/libs/i386/ChemmineOB.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)

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.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/ChemmineOB.Rcheck/00check.log'
for details.

ChemmineOB.Rcheck/00install.out:


install for i386

* installing *source* package 'ChemmineOB' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"  -Ic:/openbabel/src/i386/include   -O2 -Wall  -mtune=core2 -c ChemmineOB.cpp -o ChemmineOB.o
ChemmineOB.cpp: In function 'SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)':
ChemmineOB.cpp:953:15: warning: variable 'p' set but not used [-Wunused-but-set-variable]
   const char *p = typeName;
               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"  -Ic:/openbabel/src/i386/include   -O2 -Wall  -mtune=core2 -c canonical.cpp -o canonical.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ChemmineOB.dll tmp.def ChemmineOB.o canonical.o -Lc:/openbabel/bin/i386/bin -lopenbabel -LC:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/ChemmineOB.buildbin-libdir/ChemmineOB/libs/i386
** R
** inst
** preparing package for lazy loading
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

install for x64

* installing *source* package 'ChemmineOB' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"  -Ic:/openbabel/src/x64/include   -O2 -Wall  -mtune=core2 -c ChemmineOB.cpp -o ChemmineOB.o
ChemmineOB.cpp: In function 'SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)':
ChemmineOB.cpp:953:15: warning: variable 'p' set but not used [-Wunused-but-set-variable]
   const char *p = typeName;
               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"  -Ic:/openbabel/src/x64/include   -O2 -Wall  -mtune=core2 -c canonical.cpp -o canonical.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ChemmineOB.dll tmp.def ChemmineOB.o canonical.o -Lc:/openbabel/bin/x64/bin -lopenbabel -LC:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/ChemmineOB.buildbin-libdir/ChemmineOB/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChemmineOB' as ChemmineOB_1.12.0.zip
* DONE (ChemmineOB)

ChemmineOB.Rcheck/examples_i386/ChemmineOB-Ex.timings:

nameusersystemelapsed
canonicalNumbering_OB0.550.030.68
convertFormat000
convertFormatFile000
exactMass_OB0.010.000.01
fingerprint_OB000
forEachMol000
prop_OB000
smartsSearch_OB0.020.000.02

ChemmineOB.Rcheck/examples_x64/ChemmineOB-Ex.timings:

nameusersystemelapsed
canonicalNumbering_OB0.820.070.90
convertFormat0.020.000.01
convertFormatFile000
exactMass_OB000
fingerprint_OB0.020.000.02
forEachMol000
prop_OB000
smartsSearch_OB000