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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 321/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineOB 1.43.0  (landing page)
Thomas Girke
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/ChemmineOB
git_branch: devel
git_last_commit: 33fd022
git_last_commit_date: 2024-04-30 10:33:08 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  ERROR    ERROR  skippedskipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  

CHECK results for ChemmineOB on palomino6

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.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ChemmineOB
Version: 1.43.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChemmineOB.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ChemmineOB_1.43.0.tar.gz
StartedAt: 2024-07-15 22:36:41 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 22:38:49 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 128.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChemmineOB.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChemmineOB.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ChemmineOB_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/ChemmineOB.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ChemmineOB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChemmineOB' version '1.43.0'
* 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 ... WARNING
Found the following significant warnings:
  c:/openbabel3/src/x64/include/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 'C:/Users/biocbuild/bbs-3.20-bioc/meat/ChemmineOB.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R                3.8Mb
    libs             7.8Mb
    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 ... 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 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 for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/ChemmineOB/libs/x64/ChemmineOB.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 7 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/ChemmineOB.Rcheck/00check.log'
for details.

Installation output

ChemmineOB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ChemmineOB
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'ChemmineOB' ...
** using staged installation

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


** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -Ic:/openbabel3/src/x64/include -IC:/openbabel3/deps/eigen-3.4.0  -DHAVE_EIGEN -DHAVE_ISFINITE -Wno-misleading-indentation -fPIC   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ChemmineOB.cpp -o ChemmineOB.o
In file included from c:/openbabel3/src/x64/include/openbabel/generic.h:31,
                 from ChemmineOB.cpp:1575:
c:/openbabel3/src/x64/include/openbabel/base.h:228:32: warning: 'virtual const std::string& OpenBabel::OBGenericData::GetValue() const' was hidden [-Woverloaded-virtual=]
  228 |     virtual const std::string &GetValue()  const
      |                                ^~~~~~~~
In file included from ChemmineOB.cpp:1576:
c:/openbabel3/src/x64/include/openbabel/griddata.h:76:12: note:   by 'OpenBabel::OBGridData::GetValue'
   76 |     double GetValue (vector3 pos) const;
      |            ^~~~~~~~
c:/openbabel3/src/x64/include/openbabel/base.h:287:21: warning: 'virtual void OpenBabel::OBBase::SetTitle(const char*)' was hidden [-Woverloaded-virtual=]
  287 |       virtual void  SetTitle(const char *) {}
      |                     ^~~~~~~~
In file included from ChemmineOB.cpp:1582:
c:/openbabel3/src/x64/include/openbabel/reaction.h:101:8: note:   by 'void OpenBabel::OBReaction::SetTitle(const std::string&)'
  101 |   void SetTitle(const std::string& title) { _title=title; }
      |        ^~~~~~~~
c:/openbabel3/src/x64/include/openbabel/base.h:286:28: warning: 'virtual const char* OpenBabel::OBBase::GetTitle(bool) const' was hidden [-Woverloaded-virtual=]
  286 |       virtual const char  *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";}
      |                            ^~~~~~~~
c:/openbabel3/src/x64/include/openbabel/reaction.h:99:15: note:   by 'std::string OpenBabel::OBReaction::GetTitle() const'
   99 |   std::string GetTitle()        const { return _title; }
      |               ^~~~~~~~
In file included from c:/openbabel3/src/x64/include/openbabel/format.h:22,
                 from c:/openbabel3/src/x64/include/openbabel/obconversion.h:37,
                 from ChemmineOB.cpp:1587:
c:/openbabel3/src/x64/include/openbabel/plugin.h:41:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
      |                                          ^~~~~~~~~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/string:49,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/stdexcept:39,
                 from ChemmineOB.cpp:1559:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
ChemmineOB.cpp: In function 'void _p_f_enum_std__ios_base__event_r_std__ios_base_int__void(std::ios_base::event, std::ios_base&, int)':
ChemmineOB.cpp:4160:7: warning: unused variable 'ecode' [-Wunused-variable]
 4160 |   int ecode = 0; arg1 = (std::ios_base::event) swigarg_arg1; arg2 = (std::ios_base *) &swigarg_arg2; arg3 = (int) swigarg_arg3;
      |       ^~~~~
ChemmineOB.cpp: In function 'SEXPREC* R_swig_new_dummy()':
ChemmineOB.cpp:13728:45: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13728 | SWIGEXPORT SEXP R_swig_new_dummy ( ) { std::binary_function< char const *,char const *,bool > *result = 0 ;
      |                                             ^~~~~~~~~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
ChemmineOB.cpp:13730:18: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13730 |   result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
      |                  ^~~~~~~~~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
ChemmineOB.cpp:13730:79: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13730 |   result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
      |                                                                               ^~~~~~~~~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
ChemmineOB.cpp: In function 'SEXPREC* R_swig_delete_dummy(SEXP)':
ChemmineOB.cpp:13734:8: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13734 |   std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
      |        ^~~~~~~~~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
ChemmineOB.cpp:13734:72: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13734 |   std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
      |                                                                        ^~~~~~~~~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
ChemmineOB.cpp:13739:34: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13739 |    arg1 = reinterpret_cast< std::binary_function< char const *,char const *,bool > * >(argp1); delete arg1; r_ans = R_NilValue;
      |                                  ^~~~~~~~~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
ChemmineOB.cpp: In function 'void* _p_OpenBabel__CharPtrLessTo_p_std__binary_functionT_char_const_p_char_const_p_bool_t(void*, int*)':
ChemmineOB.cpp:39656:27: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
39656 |     return (void *)((std::binary_function< char const *,char const *,bool > *)  ((OpenBabel::CharPtrLess *) x));
      |                           ^~~~~~~~~~~~~~~
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -Ic:/openbabel3/src/x64/include -IC:/openbabel3/deps/eigen-3.4.0  -DHAVE_EIGEN -DHAVE_ISFINITE -Wno-misleading-indentation -fPIC   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c canonical.cpp -o canonical.o
In file included from c:/openbabel3/src/x64/include/openbabel/op.h:25,
                 from canonical.cpp:3:
c:/openbabel3/src/x64/include/openbabel/plugin.h:41:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
      |                                          ^~~~~~~~~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/string:49,
                 from c:/openbabel3/src/x64/include/openbabel/op.h:23:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o ChemmineOB.dll tmp.def ChemmineOB.o canonical.o -Lc:/openbabel3/bin/x64/bin -lopenbabel -LC:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-ChemmineOB/00new/ChemmineOB/libs/x64
** 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
** 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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> if(ChemmineOB:::.supportedPlatform()){
+   BiocGenerics:::testPackage("ChemmineOB")
+ }else{
+   message("Not running tests on unsupported platform ", .Platform$OS, " ", .Platform$r_arch)
+ }
[1] "test1\n OpenBabel07152422382D\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\r\n"
[1] "OC(=O)C(Br)(Cl)N\ttest1\r\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 36 35 38 39 42 41 44 43 31 20 21 13 14 28 26 10
[51] 11 45 52 51 53 54  1 56 59 60 61

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

==============================
*** Open Babel Error  in GetStringValue
  InChIFormat is not loaded
==============================
*** Open Babel Error  in GetStringValue
  InChIFormat is not loaded
==============================
*** Open Babel Error  in GetStringValue
  InChIFormat is not loaded
==============================
*** Open Babel Error  in GetStringValue
  InChIFormat is not loaded
==============================
*** Open Babel Error  in GetStringValue
  InChIFormat is not loaded
==============================
*** Open Babel Error  in GetStringValue
  InChIFormat is not loaded
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 -- Mon Jul 15 22:38:42 2024 
*********************************************** 
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 
   2.78    0.56    2.85

Example timings

ChemmineOB.Rcheck/ChemmineOB-Ex.timings

nameusersystemelapsed
canonicalNumbering_OB000
convertFormat000
convertFormatFile000
convertToImage000
exactMass_OB000
fingerprint_OB000
forEachMol000
prop_OB000
smartsSearch_OB000