Back to Multiple platform build/check report for BioC 3.21:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-01-04 11:41 -0500 (Sat, 04 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4756
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4475
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4435
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4390
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4383
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 321/2275HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineOB 1.45.0  (landing page)
Thomas Girke
Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025)
git_url: https://git.bioconductor.org/packages/ChemmineOB
git_branch: devel
git_last_commit: e269adf
git_last_commit_date: 2024-10-29 09:47:40 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped

CHECK results for ChemmineOB on palomino7

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: 1.45.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChemmineOB.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ChemmineOB_1.45.0.tar.gz
StartedAt: 2025-01-03 23:23:27 -0500 (Fri, 03 Jan 2025)
EndedAt: 2025-01-03 23:26:30 -0500 (Fri, 03 Jan 2025)
EllapsedTime: 182.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChemmineOB.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChemmineOB.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ChemmineOB_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/ChemmineOB.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 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 '1.45.0'
* 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 'E:/biocbuild/bbs-3.21-bioc/meat/ChemmineOB.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking installed package size ... INFO
  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 'E:/biocbuild/bbs-3.21-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)
File 'ChemmineOB/libs/x64/ChemmineOB.dll':
  Found non-API calls to R: 'SET_S4_OBJECT', 'STRING_PTR'

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.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
* 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, 6 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/ChemmineOB.Rcheck/00check.log'
for details.

Installation output

ChemmineOB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL ChemmineOB
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-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) 13.3.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-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\13.3.0\include\c++\string:49,
                 from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\stdexcept:39,
                 from ChemmineOB.cpp:1559:
c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\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\13.3.0\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\13.3.0\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\13.3.0\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\13.3.0\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\13.3.0\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\13.3.0\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\13.3.0\include\c++\bits\stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-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\13.3.0\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\13.3.0\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 -LE:/biocbuild/bbs-3.21-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 -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 OpenBabel01032523262D\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 41 42 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 -- Fri Jan  3 23:26:18 2025 
*********************************************** 
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 
   4.04    0.70    4.12

Example timings

ChemmineOB.Rcheck/ChemmineOB-Ex.timings

nameusersystemelapsed
canonicalNumbering_OB0.000.000.01
convertFormat000
convertFormatFile000
convertToImage000
exactMass_OB000
fingerprint_OB000
forEachMol000
prop_OB000
smartsSearch_OB000