Back to Build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-05-31 05:44:31 -0000 (Wed, 31 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4219
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CHECK results for ChemmineOB on kunpeng1


To the developers/maintainers of the ChemmineOB package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChemmineOB.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 313/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineOB 1.39.0  (landing page)
Thomas Girke
Snapshot Date: 2023-05-29 10:19:22 -0000 (Mon, 29 May 2023)
git_url: https://git.bioconductor.org/packages/ChemmineOB
git_branch: devel
git_last_commit: 745ef53
git_last_commit_date: 2023-04-25 14:28:25 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    WARNINGS  

Summary

Package: ChemmineOB
Version: 1.39.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ChemmineOB.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ChemmineOB_1.39.0.tar.gz
StartedAt: 2023-05-30 03:08:26 -0000 (Tue, 30 May 2023)
EndedAt: 2023-05-30 03:10:28 -0000 (Tue, 30 May 2023)
EllapsedTime: 122.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChemmineOB.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ChemmineOB.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ChemmineOB_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ChemmineOB.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ChemmineOB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineOB’ version ‘1.39.0’
* 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 ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* checking installed package size ... NOTE
  installed size is 22.7Mb
  sub-directories of 1Mb or more:
    R                3.8Mb
    libs            16.8Mb
    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 loading without being on the library search path ... OK
* checking 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 ‘/home/biocbuild/R/R-4.3.0/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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ChemmineOB.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ChemmineOB.Rcheck/00check.log’
for details.

Installation output

ChemmineOB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL ChemmineOB
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘ChemmineOB’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENBABEL... no
checking for OPENBABEL... no
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/include/openbabel3  -I/usr/include/eigen3  -DUSE_BOOST -DHAVE_EIGEN  -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3    -I'/home/biocbuild/R/R-4.3.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -c ChemmineOB.cpp -o ChemmineOB.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/include/openbabel3  -I/usr/include/eigen3  -DUSE_BOOST -DHAVE_EIGEN  -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3    -I'/home/biocbuild/R/R-4.3.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I/usr/local/include    -fPIC  -g -O2  -c canonical.cpp -o canonical.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o ChemmineOB.so ChemmineOB.o canonical.o -L/usr/local/lib/openbabel3 -lopenbabel -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-ChemmineOB/00new/ChemmineOB/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘copyToR’ with signature ‘"_p_std::char_traits<(char)>"’: no definition for class “_p_std::char_traits<(char)>”
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::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::OBStereo"’: no definition for class “_p_OpenBabel::OBStereo”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBStereoUnit"’: no definition for class “_p_OpenBabel::OBStereoUnit”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::LineSearchType"’: no definition for class “_p_OpenBabel::LineSearchType”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBTetrahedralConfig"’: no definition for class “_p_OpenBabel::OBTetrahedralConfig”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBCisTransConfig"’: no definition for class “_p_OpenBabel::OBCisTransConfig”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBSquarePlanarConfig"’: no definition for class “_p_OpenBabel::OBSquarePlanarConfig”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChemmineOB)

Tests output

ChemmineOB.Rcheck/tests/runTests.Rout


R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if(ChemmineOB:::.supportedPlatform()){
+   BiocGenerics:::testPackage("ChemmineOB")
+ }else{
+   message("Not running tests on unsupported platform ", .Platform$OS, " ", .Platform$r_arch)
+ }
[1] "test1\n OpenBabel05302303102D\n\n  7  6  0  0  1  0  0  0  0  0999 V2000\n    0.8660   -2.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.8660   -1.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.7321   -1.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000   -1.0000    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0\n   -1.0000   -1.0000    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0\n   -0.5000   -1.8660    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  2  3  2  0  0  0  0\n  2  4  1  0  0  0  0\n  4  5  1  0  0  0  0\n  4  6  1  0  0  0  0\n  4  7  1  0  0  0  0\nM  END\n$$$$\n"
[1] "OC(=O)C(Br)(Cl)N\ttest1\n"
[1] "OC(=O)C(Br)(Cl)N\ttest1\n"
[1] "labels:"
[[1]]
 [1] 25 47 48 16  6 55 24 15  2  7 30 33 34 37 40 19 17 18 12  9 23 22 29  5 46
[26] 27 49 50  3  4  8 57 58 32 35 36 38 39 41 42 44 43 31 20 21 13 14 28 26 10
[51] 11 45 51 52 53 54  1 56 59 60 61

650001 mass: 456.200884636001
==============================
*** Open Babel Warning  in ParseSmiles
  Failed to kekulize aromatic SMILES

start of smartsOB
==============================
*** Open Babel Warning  in ParseSmiles
  Failed to kekulize aromatic SMILES

before smartsSearch_OB
rotable bonds:
CMP1 CMP2 CMP3 CMP4 CMP5 
  24   20   14   30   10 
sdfid: 
[1] "650001" "650002" "650003" "650004" "650005"
checking equals...


RUNIT TEST PROTOCOL -- Tue May 30 03:10:22 2023 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ChemmineOB RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  4.141   0.175   4.464

Example timings

ChemmineOB.Rcheck/ChemmineOB-Ex.timings

nameusersystemelapsed
canonicalNumbering_OB0.0010.0000.000
convertFormat000
convertFormatFile000
convertToImage000
exactMass_OB000
fingerprint_OB000
forEachMol000
prop_OB0.0000.0000.001
smartsSearch_OB000