Thomas Girke
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/ChemmineOB |
| git_branch: RELEASE_3_16 |
| git_last_commit: 666338d |
| git_last_commit_date: 2022-11-01 11:08:37 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:02 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the ChemmineOB package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 303/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChemmineOB 1.36.0 (landing page) Thomas Girke
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: ChemmineOB |
| Version: 1.36.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChemmineOB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChemmineOB_1.36.0.tar.gz |
| StartedAt: 2023-04-10 19:20:08 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 19:21:40 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 92.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChemmineOB.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChemmineOB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChemmineOB_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/ChemmineOB.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChemmineOB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineOB’ version ‘1.36.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChemmineOB’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.5Mb
sub-directories of 1Mb or more:
R 3.8Mb
libs 3.6Mb
openbabel_data 2.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘ChemmineR’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘BiocGenerics’ ‘Rcpp’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls without 'PACKAGE' argument:
.Call("R_SWIG_R_pushCallbackFunctionData", ...)
.Call("R_SWIG_debug_getCallbackFunctionData", ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
cerr: no visible global function definition for ‘cerr_set’
cin: no visible global function definition for ‘cin_set’
clog: no visible global function definition for ‘clog_set’
cout: no visible global function definition for ‘cout_set’
delete,_p_OpenBabel__AliasData: no visible global function definition
for ‘delete_OpenBabel__AliasData’
delete,_p_OpenBabel__CharPtrLess: no visible global function definition
for ‘delete_OpenBabel__CharPtrLess’
delete,_p_OpenBabel__FastSearch: no visible global function definition
for ‘delete_OpenBabel__FastSearch’
delete,_p_OpenBabel__FastSearchIndexer: no visible global function
definition for ‘delete_OpenBabel__FastSearchIndexer’
delete,_p_OpenBabel__FptIndexHeader: no visible global function
definition for ‘delete_OpenBabel__FptIndexHeader’
delete,_p_OpenBabel__LineSearchType: no visible global function
definition for ‘delete_OpenBabel__LineSearchType’
delete,_p_OpenBabel__OBAlign: no visible global function definition for
‘delete_OpenBabel__OBAlign’
delete,_p_OpenBabel__OBAngle: no visible global function definition for
‘delete_OpenBabel__OBAngle’
delete,_p_OpenBabel__OBAngleData: no visible global function definition
for ‘delete_OpenBabel__OBAngleData’
delete,_p_OpenBabel__OBAromaticTyper: no visible global function
definition for ‘delete_OpenBabel__OBAromaticTyper’
delete,_p_OpenBabel__OBAtom: no visible global function definition for
‘delete_OpenBabel__OBAtom’
delete,_p_OpenBabel__OBAtomAtomIter: no visible global function
definition for ‘delete_OpenBabel__OBAtomAtomIter’
delete,_p_OpenBabel__OBAtomBondIter: no visible global function
definition for ‘delete_OpenBabel__OBAtomBondIter’
delete,_p_OpenBabel__OBAtomHOF: no visible global function definition
for ‘delete_OpenBabel__OBAtomHOF’
delete,_p_OpenBabel__OBAtomTyper: no visible global function definition
for ‘delete_OpenBabel__OBAtomTyper’
delete,_p_OpenBabel__OBAtomicHeatOfFormationTable: no visible global
function definition for
‘delete_OpenBabel__OBAtomicHeatOfFormationTable’
delete,_p_OpenBabel__OBBase: no visible global function definition for
‘delete_OpenBabel__OBBase’
delete,_p_OpenBabel__OBBitVec: no visible global function definition
for ‘delete_OpenBabel__OBBitVec’
delete,_p_OpenBabel__OBBond: no visible global function definition for
‘delete_OpenBabel__OBBond’
delete,_p_OpenBabel__OBBuilder: no visible global function definition
for ‘delete_OpenBabel__OBBuilder’
delete,_p_OpenBabel__OBChainsParser: no visible global function
definition for ‘delete_OpenBabel__OBChainsParser’
delete,_p_OpenBabel__OBChargeModel: no visible global function
definition for ‘delete_OpenBabel__OBChargeModel’
delete,_p_OpenBabel__OBCisTransConfig: no visible global function
definition for ‘delete_OpenBabel__OBCisTransConfig’
delete,_p_OpenBabel__OBCisTransStereo: no visible global function
definition for ‘delete_OpenBabel__OBCisTransStereo’
delete,_p_OpenBabel__OBCommentData: no visible global function
definition for ‘delete_OpenBabel__OBCommentData’
delete,_p_OpenBabel__OBConformerData: no visible global function
definition for ‘delete_OpenBabel__OBConformerData’
delete,_p_OpenBabel__OBConformerFilter: no visible global function
definition for ‘delete_OpenBabel__OBConformerFilter’
delete,_p_OpenBabel__OBConformerFilters: no visible global function
definition for ‘delete_OpenBabel__OBConformerFilters’
delete,_p_OpenBabel__OBConformerScore: no visible global function
definition for ‘delete_OpenBabel__OBConformerScore’
delete,_p_OpenBabel__OBConformerSearch: no visible global function
definition for ‘delete_OpenBabel__OBConformerSearch’
delete,_p_OpenBabel__OBConversion: no visible global function
definition for ‘delete_OpenBabel__OBConversion’
delete,_p_OpenBabel__OBDOSData: no visible global function definition
for ‘delete_OpenBabel__OBDOSData’
delete,_p_OpenBabel__OBDescriptor: no visible global function
definition for ‘delete_OpenBabel__OBDescriptor’
delete,_p_OpenBabel__OBElectronicTransitionData: no visible global
function definition for
‘delete_OpenBabel__OBElectronicTransitionData’
delete,_p_OpenBabel__OBEnergyConformerScore: no visible global function
definition for ‘delete_OpenBabel__OBEnergyConformerScore’
delete,_p_OpenBabel__OBError: no visible global function definition for
‘delete_OpenBabel__OBError’
delete,_p_OpenBabel__OBExternalBond: no visible global function
definition for ‘delete_OpenBabel__OBExternalBond’
delete,_p_OpenBabel__OBExternalBondData: no visible global function
definition for ‘delete_OpenBabel__OBExternalBondData’
delete,_p_OpenBabel__OBFFCalculation2: no visible global function
definition for ‘delete_OpenBabel__OBFFCalculation2’
delete,_p_OpenBabel__OBFFCalculation3: no visible global function
definition for ‘delete_OpenBabel__OBFFCalculation3’
delete,_p_OpenBabel__OBFFCalculation4: no visible global function
definition for ‘delete_OpenBabel__OBFFCalculation4’
delete,_p_OpenBabel__OBFFConstraint: no visible global function
definition for ‘delete_OpenBabel__OBFFConstraint’
delete,_p_OpenBabel__OBFFConstraints: no visible global function
definition for ‘delete_OpenBabel__OBFFConstraints’
delete,_p_OpenBabel__OBFFParameter: no visible global function
definition for ‘delete_OpenBabel__OBFFParameter’
delete,_p_OpenBabel__OBFingerprint: no visible global function
definition for ‘delete_OpenBabel__OBFingerprint’
delete,_p_OpenBabel__OBForceField: no visible global function
definition for ‘delete_OpenBabel__OBForceField’
delete,_p_OpenBabel__OBFormat: no visible global function definition
for ‘delete_OpenBabel__OBFormat’
delete,_p_OpenBabel__OBFreeGrid: no visible global function definition
for ‘delete_OpenBabel__OBFreeGrid’
delete,_p_OpenBabel__OBFreeGridPoint: no visible global function
definition for ‘delete_OpenBabel__OBFreeGridPoint’
delete,_p_OpenBabel__OBGenericData: no visible global function
definition for ‘delete_OpenBabel__OBGenericData’
delete,_p_OpenBabel__OBGlobalDataBase: no visible global function
definition for ‘delete_OpenBabel__OBGlobalDataBase’
delete,_p_OpenBabel__OBGraphSym: no visible global function definition
for ‘delete_OpenBabel__OBGraphSym’
delete,_p_OpenBabel__OBGridData: no visible global function definition
for ‘delete_OpenBabel__OBGridData’
delete,_p_OpenBabel__OBInternalCoord: no visible global function
definition for ‘delete_OpenBabel__OBInternalCoord’
delete,_p_OpenBabel__OBIsomorphismMapper: no visible global function
definition for ‘delete_OpenBabel__OBIsomorphismMapper’
delete,_p_OpenBabel__OBMatrixData: no visible global function
definition for ‘delete_OpenBabel__OBMatrixData’
delete,_p_OpenBabel__OBMessageHandler: no visible global function
definition for ‘delete_OpenBabel__OBMessageHandler’
delete,_p_OpenBabel__OBMinimizingEnergyConformerScore: no visible
global function definition for
‘delete_OpenBabel__OBMinimizingEnergyConformerScore’
delete,_p_OpenBabel__OBMinimizingRMSDConformerScore: no visible global
function definition for
‘delete_OpenBabel__OBMinimizingRMSDConformerScore’
delete,_p_OpenBabel__OBMol: no visible global function definition for
‘delete_OpenBabel__OBMol’
delete,_p_OpenBabel__OBMolAngleIter: no visible global function
definition for ‘delete_OpenBabel__OBMolAngleIter’
delete,_p_OpenBabel__OBMolAtomBFSIter: no visible global function
definition for ‘delete_OpenBabel__OBMolAtomBFSIter’
delete,_p_OpenBabel__OBMolAtomDFSIter: no visible global function
definition for ‘delete_OpenBabel__OBMolAtomDFSIter’
delete,_p_OpenBabel__OBMolAtomIter: no visible global function
definition for ‘delete_OpenBabel__OBMolAtomIter’
delete,_p_OpenBabel__OBMolBondBFSIter: no visible global function
definition for ‘delete_OpenBabel__OBMolBondBFSIter’
delete,_p_OpenBabel__OBMolBondIter: no visible global function
definition for ‘delete_OpenBabel__OBMolBondIter’
delete,_p_OpenBabel__OBMolPairIter: no visible global function
definition for ‘delete_OpenBabel__OBMolPairIter’
delete,_p_OpenBabel__OBMolRingIter: no visible global function
definition for ‘delete_OpenBabel__OBMolRingIter’
delete,_p_OpenBabel__OBMolTorsionIter: no visible global function
definition for ‘delete_OpenBabel__OBMolTorsionIter’
delete,_p_OpenBabel__OBOp: no visible global function definition for
‘delete_OpenBabel__OBOp’
delete,_p_OpenBabel__OBOrbital: no visible global function definition
for ‘delete_OpenBabel__OBOrbital’
delete,_p_OpenBabel__OBOrbitalData: no visible global function
definition for ‘delete_OpenBabel__OBOrbitalData’
delete,_p_OpenBabel__OBPairData: no visible global function definition
for ‘delete_OpenBabel__OBPairData’
delete,_p_OpenBabel__OBPcharge: no visible global function definition
for ‘delete_OpenBabel__OBPcharge’
delete,_p_OpenBabel__OBPlugin: no visible global function definition
for ‘delete_OpenBabel__OBPlugin’
delete,_p_OpenBabel__OBQuery: no visible global function definition for
‘delete_OpenBabel__OBQuery’
delete,_p_OpenBabel__OBQueryAtom: no visible global function definition
for ‘delete_OpenBabel__OBQueryAtom’
delete,_p_OpenBabel__OBQueryBond: no visible global function definition
for ‘delete_OpenBabel__OBQueryBond’
delete,_p_OpenBabel__OBRMSDConformerScore: no visible global function
definition for ‘delete_OpenBabel__OBRMSDConformerScore’
delete,_p_OpenBabel__OBRTree: no visible global function definition for
‘delete_OpenBabel__OBRTree’
delete,_p_OpenBabel__OBReaction: no visible global function definition
for ‘delete_OpenBabel__OBReaction’
delete,_p_OpenBabel__OBResidue: no visible global function definition
for ‘delete_OpenBabel__OBResidue’
delete,_p_OpenBabel__OBResidueAtomIter: no visible global function
definition for ‘delete_OpenBabel__OBResidueAtomIter’
delete,_p_OpenBabel__OBResidueData: no visible global function
definition for ‘delete_OpenBabel__OBResidueData’
delete,_p_OpenBabel__OBResidueIter: no visible global function
definition for ‘delete_OpenBabel__OBResidueIter’
delete,_p_OpenBabel__OBRing: no visible global function definition for
‘delete_OpenBabel__OBRing’
delete,_p_OpenBabel__OBRingData: no visible global function definition
for ‘delete_OpenBabel__OBRingData’
delete,_p_OpenBabel__OBRingSearch: no visible global function
definition for ‘delete_OpenBabel__OBRingSearch’
delete,_p_OpenBabel__OBRingTyper: no visible global function definition
for ‘delete_OpenBabel__OBRingTyper’
delete,_p_OpenBabel__OBRotamerList: no visible global function
definition for ‘delete_OpenBabel__OBRotamerList’
delete,_p_OpenBabel__OBRotationData: no visible global function
definition for ‘delete_OpenBabel__OBRotationData’
delete,_p_OpenBabel__OBRotor: no visible global function definition for
‘delete_OpenBabel__OBRotor’
delete,_p_OpenBabel__OBRotorKeys: no visible global function definition
for ‘delete_OpenBabel__OBRotorKeys’
delete,_p_OpenBabel__OBRotorList: no visible global function definition
for ‘delete_OpenBabel__OBRotorList’
delete,_p_OpenBabel__OBRotorRule: no visible global function definition
for ‘delete_OpenBabel__OBRotorRule’
delete,_p_OpenBabel__OBRotorRules: no visible global function
definition for ‘delete_OpenBabel__OBRotorRules’
delete,_p_OpenBabel__OBSSMatch: no visible global function definition
for ‘delete_OpenBabel__OBSSMatch’
delete,_p_OpenBabel__OBSerialNums: no visible global function
definition for ‘delete_OpenBabel__OBSerialNums’
delete,_p_OpenBabel__OBSetData: no visible global function definition
for ‘delete_OpenBabel__OBSetData’
delete,_p_OpenBabel__OBSmartsMatcher: no visible global function
definition for ‘delete_OpenBabel__OBSmartsMatcher’
delete,_p_OpenBabel__OBSmartsPattern: no visible global function
definition for ‘delete_OpenBabel__OBSmartsPattern’
delete,_p_OpenBabel__OBSpectrophore: no visible global function
definition for ‘delete_OpenBabel__OBSpectrophore’
delete,_p_OpenBabel__OBSqrtTbl: no visible global function definition
for ‘delete_OpenBabel__OBSqrtTbl’
delete,_p_OpenBabel__OBSquarePlanarConfig: no visible global function
definition for ‘delete_OpenBabel__OBSquarePlanarConfig’
delete,_p_OpenBabel__OBSquarePlanarStereo: no visible global function
definition for ‘delete_OpenBabel__OBSquarePlanarStereo’
delete,_p_OpenBabel__OBStereo: no visible global function definition
for ‘delete_OpenBabel__OBStereo’
delete,_p_OpenBabel__OBStereoBase: no visible global function
definition for ‘delete_OpenBabel__OBStereoBase’
delete,_p_OpenBabel__OBStereoFacade: no visible global function
definition for ‘delete_OpenBabel__OBStereoFacade’
delete,_p_OpenBabel__OBStereoUnit: no visible global function
definition for ‘delete_OpenBabel__OBStereoUnit’
delete,_p_OpenBabel__OBStericConformerFilter: no visible global
function definition for ‘delete_OpenBabel__OBStericConformerFilter’
delete,_p_OpenBabel__OBStopwatch: no visible global function definition
for ‘delete_OpenBabel__OBStopwatch’
delete,_p_OpenBabel__OBSymmetryData: no visible global function
definition for ‘delete_OpenBabel__OBSymmetryData’
delete,_p_OpenBabel__OBTetraNonPlanarStereo: no visible global function
definition for ‘delete_OpenBabel__OBTetraNonPlanarStereo’
delete,_p_OpenBabel__OBTetraPlanarStereo: no visible global function
definition for ‘delete_OpenBabel__OBTetraPlanarStereo’
delete,_p_OpenBabel__OBTetrahedralConfig: no visible global function
definition for ‘delete_OpenBabel__OBTetrahedralConfig’
delete,_p_OpenBabel__OBTetrahedralStereo: no visible global function
definition for ‘delete_OpenBabel__OBTetrahedralStereo’
delete,_p_OpenBabel__OBTorsion: no visible global function definition
for ‘delete_OpenBabel__OBTorsion’
delete,_p_OpenBabel__OBTorsionData: no visible global function
definition for ‘delete_OpenBabel__OBTorsionData’
delete,_p_OpenBabel__OBTypeTable: no visible global function definition
for ‘delete_OpenBabel__OBTypeTable’
delete,_p_OpenBabel__OBUnitCell: no visible global function definition
for ‘delete_OpenBabel__OBUnitCell’
delete,_p_OpenBabel__OBVectorData: no visible global function
definition for ‘delete_OpenBabel__OBVectorData’
delete,_p_OpenBabel__OBVibrationData: no visible global function
definition for ‘delete_OpenBabel__OBVibrationData’
delete,_p_OpenBabel__OBVirtualBond: no visible global function
definition for ‘delete_OpenBabel__OBVirtualBond’
delete,_p_OpenBabel__SpaceGroup: no visible global function definition
for ‘delete_OpenBabel__SpaceGroup’
delete,_p_OpenBabel__matrix3x3: no visible global function definition
for ‘delete_OpenBabel__matrix3x3’
delete,_p_OpenBabel__obLogBuf: no visible global function definition
for ‘delete_OpenBabel__obLogBuf’
delete,_p_OpenBabel__rotor_digit: no visible global function definition
for ‘delete_OpenBabel__rotor_digit’
delete,_p_OpenBabel__transform3d: no visible global function definition
for ‘delete_OpenBabel__transform3d’
delete,_p_OpenBabel__vector3: no visible global function definition for
‘delete_OpenBabel__vector3’
delete,_p_std__basic_iosT_char_std__char_traitsT_char_t_t: no visible
global function definition for
‘delete_std__basic_iosT_char_std__char_traitsT_char_t_t’
delete,_p_std__basic_iostreamT_char_std__char_traitsT_char_t_t: no
visible global function definition for
‘delete_std__basic_iostreamT_char_std__char_traitsT_char_t_t’
delete,_p_std__basic_istreamT_char_std__char_traitsT_char_t_t: no
visible global function definition for
‘delete_std__basic_istreamT_char_std__char_traitsT_char_t_t’
delete,_p_std__basic_ostreamT_char_std__char_traitsT_char_t_t: no
visible global function definition for
‘delete_std__basic_ostreamT_char_std__char_traitsT_char_t_t’
delete,_p_std__binary_functionT_char_const_p_char_const_p_bool_t: no
visible global function definition for
‘delete_std__binary_functionT_char_const_p_char_const_p_bool_t’
delete,_p_std__ios_base: no visible global function definition for
‘delete_std__ios_base’
delete,_p_std__pairT_unsigned_int_unsigned_int_t: no visible global
function definition for
‘delete_std__pairT_unsigned_int_unsigned_int_t’
delete,_p_std__stringbuf: no visible global function definition for
‘delete_std__stringbuf’
delete,_p_std__vectorT_OpenBabel__OBBond_std__allocatorT_OpenBabel__OBBond_t_t:
no visible global function definition for
‘delete_std__vectorT_OpenBabel__OBBond_std__allocatorT_OpenBabel__OBBond_t_t’
delete,_p_std__vectorT_OpenBabel__OBGenericData_p_std__allocatorT_OpenBabel__OBGenericData_p_t_t:
no visible global function definition for
‘delete_std__vectorT_OpenBabel__OBGenericData_p_std__allocatorT_OpenBabel__OBGenericData_p_t_t’
delete,_p_std__vectorT_OpenBabel__OBInternalCoord_p_std__allocatorT_OpenBabel__OBInternalCoord_p_t_t:
no visible global function definition for
‘delete_std__vectorT_OpenBabel__OBInternalCoord_p_std__allocatorT_OpenBabel__OBInternalCoord_p_t_t’
delete,_p_std__vectorT_OpenBabel__OBMol_std__allocatorT_OpenBabel__OBMol_t_t:
no visible global function definition for
‘delete_std__vectorT_OpenBabel__OBMol_std__allocatorT_OpenBabel__OBMol_t_t’
delete,_p_std__vectorT_OpenBabel__OBResidue_std__allocatorT_OpenBabel__OBResidue_t_t:
no visible global function definition for
‘delete_std__vectorT_OpenBabel__OBResidue_std__allocatorT_OpenBabel__OBResidue_t_t’
delete,_p_std__vectorT_OpenBabel__OBRing_p_std__allocatorT_OpenBabel__OBRing_p_t_t:
no visible global function definition for
‘delete_std__vectorT_OpenBabel__OBRing_p_std__allocatorT_OpenBabel__OBRing_p_t_t’
delete,_p_std__vectorT_OpenBabel__OBRing_std__allocatorT_OpenBabel__OBRing_t_t:
no visible global function definition for
‘delete_std__vectorT_OpenBabel__OBRing_std__allocatorT_OpenBabel__OBRing_t_t’
delete,_p_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t:
no visible global function definition for
‘delete_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t’
delete,_p_std__vectorT_double_std__allocatorT_double_t_t: no visible
global function definition for
‘delete_std__vectorT_double_std__allocatorT_double_t_t’
delete,_p_std__vectorT_int_std__allocatorT_int_t_t: no visible global
function definition for
‘delete_std__vectorT_int_std__allocatorT_int_t_t’
delete,_p_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t:
no visible global function definition for
‘delete_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t’
delete,_p_std__vectorT_std__string_std__allocatorT_std__string_t_t: no
visible global function definition for
‘delete_std__vectorT_std__string_std__allocatorT_std__string_t_t’
delete,_p_std__vectorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_std__allocatorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_t_t:
no visible global function definition for
‘delete_std__vectorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_std__allocatorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_t_t’
delete,_p_std__vectorT_std__vectorT_int_std__allocatorT_int_t_t_std__allocatorT_std__vectorT_int_std__allocatorT_int_t_t_t_t:
no visible global function definition for
‘delete_std__vectorT_std__vectorT_int_std__allocatorT_int_t_t_std__allocatorT_std__vectorT_int_std__allocatorT_int_t_t_t_t’
delete,_p_std__vectorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_std__allocatorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_t_t:
no visible global function definition for
‘delete_std__vectorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_std__allocatorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_t_t’
delete,_p_std__vectorT_unsigned_int_std__allocatorT_unsigned_int_t_t:
no visible global function definition for
‘delete_std__vectorT_unsigned_int_std__allocatorT_unsigned_int_t_t’
Undefined global functions or variables:
cerr_set cin_set clog_set cout_set delete_OpenBabel__AliasData
delete_OpenBabel__CharPtrLess delete_OpenBabel__FastSearch
delete_OpenBabel__FastSearchIndexer delete_OpenBabel__FptIndexHeader
delete_OpenBabel__LineSearchType delete_OpenBabel__OBAlign
delete_OpenBabel__OBAngle delete_OpenBabel__OBAngleData
delete_OpenBabel__OBAromaticTyper delete_OpenBabel__OBAtom
delete_OpenBabel__OBAtomAtomIter delete_OpenBabel__OBAtomBondIter
delete_OpenBabel__OBAtomHOF delete_OpenBabel__OBAtomTyper
delete_OpenBabel__OBAtomicHeatOfFormationTable
delete_OpenBabel__OBBase delete_OpenBabel__OBBitVec
delete_OpenBabel__OBBond delete_OpenBabel__OBBuilder
delete_OpenBabel__OBChainsParser delete_OpenBabel__OBChargeModel
delete_OpenBabel__OBCisTransConfig delete_OpenBabel__OBCisTransStereo
delete_OpenBabel__OBCommentData delete_OpenBabel__OBConformerData
delete_OpenBabel__OBConformerFilter
delete_OpenBabel__OBConformerFilters
delete_OpenBabel__OBConformerScore
delete_OpenBabel__OBConformerSearch delete_OpenBabel__OBConversion
delete_OpenBabel__OBDOSData delete_OpenBabel__OBDescriptor
delete_OpenBabel__OBElectronicTransitionData
delete_OpenBabel__OBEnergyConformerScore delete_OpenBabel__OBError
delete_OpenBabel__OBExternalBond delete_OpenBabel__OBExternalBondData
delete_OpenBabel__OBFFCalculation2 delete_OpenBabel__OBFFCalculation3
delete_OpenBabel__OBFFCalculation4 delete_OpenBabel__OBFFConstraint
delete_OpenBabel__OBFFConstraints delete_OpenBabel__OBFFParameter
delete_OpenBabel__OBFingerprint delete_OpenBabel__OBForceField
delete_OpenBabel__OBFormat delete_OpenBabel__OBFreeGrid
delete_OpenBabel__OBFreeGridPoint delete_OpenBabel__OBGenericData
delete_OpenBabel__OBGlobalDataBase delete_OpenBabel__OBGraphSym
delete_OpenBabel__OBGridData delete_OpenBabel__OBInternalCoord
delete_OpenBabel__OBIsomorphismMapper delete_OpenBabel__OBMatrixData
delete_OpenBabel__OBMessageHandler
delete_OpenBabel__OBMinimizingEnergyConformerScore
delete_OpenBabel__OBMinimizingRMSDConformerScore
delete_OpenBabel__OBMol delete_OpenBabel__OBMolAngleIter
delete_OpenBabel__OBMolAtomBFSIter delete_OpenBabel__OBMolAtomDFSIter
delete_OpenBabel__OBMolAtomIter delete_OpenBabel__OBMolBondBFSIter
delete_OpenBabel__OBMolBondIter delete_OpenBabel__OBMolPairIter
delete_OpenBabel__OBMolRingIter delete_OpenBabel__OBMolTorsionIter
delete_OpenBabel__OBOp delete_OpenBabel__OBOrbital
delete_OpenBabel__OBOrbitalData delete_OpenBabel__OBPairData
delete_OpenBabel__OBPcharge delete_OpenBabel__OBPlugin
delete_OpenBabel__OBQuery delete_OpenBabel__OBQueryAtom
delete_OpenBabel__OBQueryBond delete_OpenBabel__OBRMSDConformerScore
delete_OpenBabel__OBRTree delete_OpenBabel__OBReaction
delete_OpenBabel__OBResidue delete_OpenBabel__OBResidueAtomIter
delete_OpenBabel__OBResidueData delete_OpenBabel__OBResidueIter
delete_OpenBabel__OBRing delete_OpenBabel__OBRingData
delete_OpenBabel__OBRingSearch delete_OpenBabel__OBRingTyper
delete_OpenBabel__OBRotamerList delete_OpenBabel__OBRotationData
delete_OpenBabel__OBRotor delete_OpenBabel__OBRotorKeys
delete_OpenBabel__OBRotorList delete_OpenBabel__OBRotorRule
delete_OpenBabel__OBRotorRules delete_OpenBabel__OBSSMatch
delete_OpenBabel__OBSerialNums delete_OpenBabel__OBSetData
delete_OpenBabel__OBSmartsMatcher delete_OpenBabel__OBSmartsPattern
delete_OpenBabel__OBSpectrophore delete_OpenBabel__OBSqrtTbl
delete_OpenBabel__OBSquarePlanarConfig
delete_OpenBabel__OBSquarePlanarStereo delete_OpenBabel__OBStereo
delete_OpenBabel__OBStereoBase delete_OpenBabel__OBStereoFacade
delete_OpenBabel__OBStereoUnit
delete_OpenBabel__OBStericConformerFilter
delete_OpenBabel__OBStopwatch delete_OpenBabel__OBSymmetryData
delete_OpenBabel__OBTetraNonPlanarStereo
delete_OpenBabel__OBTetraPlanarStereo
delete_OpenBabel__OBTetrahedralConfig
delete_OpenBabel__OBTetrahedralStereo delete_OpenBabel__OBTorsion
delete_OpenBabel__OBTorsionData delete_OpenBabel__OBTypeTable
delete_OpenBabel__OBUnitCell delete_OpenBabel__OBVectorData
delete_OpenBabel__OBVibrationData delete_OpenBabel__OBVirtualBond
delete_OpenBabel__SpaceGroup delete_OpenBabel__matrix3x3
delete_OpenBabel__obLogBuf delete_OpenBabel__rotor_digit
delete_OpenBabel__transform3d delete_OpenBabel__vector3
delete_std__basic_iosT_char_std__char_traitsT_char_t_t
delete_std__basic_iostreamT_char_std__char_traitsT_char_t_t
delete_std__basic_istreamT_char_std__char_traitsT_char_t_t
delete_std__basic_ostreamT_char_std__char_traitsT_char_t_t
delete_std__binary_functionT_char_const_p_char_const_p_bool_t
delete_std__ios_base delete_std__pairT_unsigned_int_unsigned_int_t
delete_std__stringbuf
delete_std__vectorT_OpenBabel__OBBond_std__allocatorT_OpenBabel__OBBond_t_t
delete_std__vectorT_OpenBabel__OBGenericData_p_std__allocatorT_OpenBabel__OBGenericData_p_t_t
delete_std__vectorT_OpenBabel__OBInternalCoord_p_std__allocatorT_OpenBabel__OBInternalCoord_p_t_t
delete_std__vectorT_OpenBabel__OBMol_std__allocatorT_OpenBabel__OBMol_t_t
delete_std__vectorT_OpenBabel__OBResidue_std__allocatorT_OpenBabel__OBResidue_t_t
delete_std__vectorT_OpenBabel__OBRing_p_std__allocatorT_OpenBabel__OBRing_p_t_t
delete_std__vectorT_OpenBabel__OBRing_std__allocatorT_OpenBabel__OBRing_t_t
delete_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t
delete_std__vectorT_double_std__allocatorT_double_t_t
delete_std__vectorT_int_std__allocatorT_int_t_t
delete_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t
delete_std__vectorT_std__string_std__allocatorT_std__string_t_t
delete_std__vectorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_std__allocatorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_t_t
delete_std__vectorT_std__vectorT_int_std__allocatorT_int_t_t_std__allocatorT_std__vectorT_int_std__allocatorT_int_t_t_t_t
delete_std__vectorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_std__allocatorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_t_t
delete_std__vectorT_unsigned_int_std__allocatorT_unsigned_int_t_t
* checking Rd files ... NOTE
prepare_Rd: canonicalNumbering_OB.Rd:30-32: Dropping empty section \note
prepare_Rd: forEachMol.Rd:48-50: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '$' and siglist '_p_OpenBabel__OBAlign'
generic '$' and siglist '_p_OpenBabel__OBAtomHOF'
generic '$' and siglist '_p_OpenBabel__OBAtomicHeatOfFormationTable'
generic '$' and siglist '_p_OpenBabel__OBChargeModel'
generic '$' and siglist '_p_OpenBabel__OBCisTransConfig'
generic '$' and siglist '_p_OpenBabel__OBCisTransStereo'
generic '$' and siglist '_p_OpenBabel__OBConformerFilter'
generic '$' and siglist '_p_OpenBabel__OBConformerScore'
generic '$' and siglist '_p_OpenBabel__OBConformerSearch'
generic '$' and siglist '_p_OpenBabel__OBEnergyConformerScore'
generic '$' and siglist '_p_OpenBabel__OBFreeGrid'
generic '$' and siglist '_p_OpenBabel__OBFreeGridPoint'
generic '$' and siglist '_p_OpenBabel__OBGraphSym'
generic '$' and siglist '_p_OpenBabel__OBIsomorphismMapper'
generic '$' and siglist
'_p_OpenBabel__OBMinimizingEnergyConformerScore'
generic '$' and siglist '_p_OpenBabel__OBPcharge'
generic '$' and siglist '_p_OpenBabel__OBQuery'
generic '$' and siglist '_p_OpenBabel__OBQueryAtom'
generic '$' and siglist '_p_OpenBabel__OBQueryBond'
generic '$' and siglist '_p_OpenBabel__OBReaction'
generic '$' and siglist '_p_OpenBabel__OBRotamerList'
generic '$' and siglist '_p_OpenBabel__OBRotor'
generic '$' and siglist '_p_OpenBabel__OBRotorKeys'
generic '$' and siglist '_p_OpenBabel__OBRotorList'
generic '$' and siglist '_p_OpenBabel__OBRotorRule'
generic '$' and siglist '_p_OpenBabel__OBRotorRules'
generic '$' and siglist '_p_OpenBabel__OBSpectrophore'
generic '$' and siglist '_p_OpenBabel__OBSquarePlanarConfig'
generic '$' and siglist '_p_OpenBabel__OBSquarePlanarStereo'
generic '$' and siglist '_p_OpenBabel__OBStereoBase'
generic '$' and siglist '_p_OpenBabel__OBStereoFacade'
generic '$' and siglist '_p_OpenBabel__OBStereoUnit'
generic '$' and siglist '_p_OpenBabel__OBTetrahedralConfig'
generic '$' and siglist '_p_OpenBabel__OBTetrahedralStereo'
generic '$' and siglist '_p_OpenBabel__rotor_digit'
generic '$' and siglist
'_p_std__basic_iosT_char_std__char_traitsT_char_t_t'
generic '$' and siglist
'_p_std__basic_istreamT_char_std__char_traitsT_char_t_t'
generic '$' and siglist
'_p_std__basic_ostreamT_char_std__char_traitsT_char_t_t'
generic '$' and siglist '_p_std__ios_base'
generic '$<-' and siglist '_p_OpenBabel__OBCisTransConfig'
generic '$<-' and siglist '_p_OpenBabel__OBSquarePlanarConfig'
generic '$<-' and siglist '_p_OpenBabel__OBStereoUnit'
generic '$<-' and siglist '_p_OpenBabel__OBTetrahedralConfig'
generic '[[<-' and siglist '_p_OpenBabel__OBCisTransConfig,character'
generic '[[<-' and siglist
'_p_OpenBabel__OBSquarePlanarConfig,character'
generic '[[<-' and siglist '_p_OpenBabel__OBStereoUnit,character'
generic '[[<-' and siglist
'_p_OpenBabel__OBTetrahedralConfig,character'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ChemmineOB/libs/ChemmineOB.so’:
Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
Found ‘_abort’, possibly from ‘abort’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 6 NOTEs
See
‘/Users/biocbuild/bbs-3.16-bioc/meat/ChemmineOB.Rcheck/00check.log’
for details.
ChemmineOB.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChemmineOB
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘ChemmineOB’ ...
** using staged installation
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENBABEL... no
checking for OPENBABEL... no
checking for gcc... clang -mmacosx-version-min=10.13
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ChemmineOB.cpp -o ChemmineOB.o
In file included from ChemmineOB.cpp:1576:
/usr/local/include/openbabel3/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual]
double GetValue(int i, int j, int k) const;
^
/usr/local/include/openbabel3/openbabel/base.h:228:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3)
virtual const std::string &GetValue() const
^
In file included from ChemmineOB.cpp:1576:
/usr/local/include/openbabel3/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual]
double GetValue (vector3 pos) const;
^
/usr/local/include/openbabel3/openbabel/base.h:228:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1)
virtual const std::string &GetValue() const
^
In file included from ChemmineOB.cpp:1582:
/usr/local/include/openbabel3/openbabel/reaction.h:99:15: warning: 'OpenBabel::OBReaction::GetTitle' hides overloaded virtual function [-Woverloaded-virtual]
std::string GetTitle() const { return _title; }
^
/usr/local/include/openbabel3/openbabel/base.h:286:28: note: hidden overloaded virtual function 'OpenBabel::OBBase::GetTitle' declared here: different number of parameters (1 vs 0)
virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";}
^
In file included from ChemmineOB.cpp:1582:
/usr/local/include/openbabel3/openbabel/reaction.h:101:8: warning: 'OpenBabel::OBReaction::SetTitle' hides overloaded virtual function [-Woverloaded-virtual]
void SetTitle(const std::string& title) { _title=title; }
^
/usr/local/include/openbabel3/openbabel/base.h:287:21: note: hidden overloaded virtual function 'OpenBabel::OBBase::SetTitle' declared here: type mismatch at 1st parameter ('const char *' vs 'const std::string &' (aka 'const basic_string<char, char_traits<char>, allocator<char>> &'))
virtual void SetTitle(const char *) {}
^
ChemmineOB.cpp:4160:7: warning: unused variable 'ecode' [-Wunused-variable]
int ecode = 0; arg1 = (std::ios_base::event) swigarg_arg1; arg2 = (std::ios_base *) &swigarg_arg2; arg3 = (int) swigarg_arg3;
^
5 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c canonical.cpp -o canonical.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ChemmineOB.so ChemmineOB.o canonical.o -L/usr/local/lib/openbabel3 -lopenbabel -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: dylib (/usr/local/lib/libopenbabel.dylib) was built for newer macOS version (12.0) than being linked (10.13)
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-ChemmineOB/00new/ChemmineOB/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘copyToR’ with signature ‘"_p_std::char_traits<(char)>"’: no definition for class “_p_std::char_traits<(char)>”
in method for ‘copyToR’ with signature ‘"_p_std::pair<(unsigned int,unsigned int)>"’: no definition for class “_p_std::pair<(unsigned int,unsigned int)>”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::CharPtrLess"’: no definition for class “_p_OpenBabel::CharPtrLess”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::FptIndexHeader"’: no definition for class “_p_OpenBabel::FptIndexHeader”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBStereo"’: no definition for class “_p_OpenBabel::OBStereo”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBStereoUnit"’: no definition for class “_p_OpenBabel::OBStereoUnit”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::LineSearchType"’: no definition for class “_p_OpenBabel::LineSearchType”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBTetrahedralConfig"’: no definition for class “_p_OpenBabel::OBTetrahedralConfig”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBCisTransConfig"’: no definition for class “_p_OpenBabel::OBCisTransConfig”
in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBSquarePlanarConfig"’: no definition for class “_p_OpenBabel::OBSquarePlanarConfig”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChemmineOB)
ChemmineOB.Rcheck/tests/runTests.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> if(ChemmineOB:::.supportedPlatform()){
+ BiocGenerics:::testPackage("ChemmineOB")
+ }else{
+ message("Not running tests on unsupported platform ", .Platform$OS, " ", .Platform$r_arch)
+ }
[1] "test1\n OpenBabel04102319212D\n\n 7 6 0 0 1 0 0 0 0 0999 V2000\n 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.7321 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0\n -1.0000 -1.0000 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0\n -0.5000 -1.8660 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 2 0 0 0 0\n 2 4 1 0 0 0 0\n 4 5 1 0 0 0 0\n 4 6 1 0 0 0 0\n 4 7 1 0 0 0 0\nM END\n$$$$\n"
[1] "OC(=O)C(Br)(Cl)N\ttest1\n"
[1] "OC(=O)C(Br)(Cl)N\ttest1\n"
[1] "labels:"
[[1]]
[1] 25 47 48 16 6 55 24 15 2 7 30 33 34 37 40 19 17 18 12 9 23 22 29 5 46
[26] 27 49 50 3 4 8 57 58 32 35 36 38 39 41 42 43 44 31 20 21 13 14 28 26 10
[51] 11 45 51 52 53 54 1 56 59 60 61
650001 mass: 456.200884636001
==============================
*** Open Babel Warning in ParseSmiles
Failed to kekulize aromatic SMILES
2023-04-10 19:21:31.097 R[89443:1009822632] XType: com.apple.fonts is not accessible.
2023-04-10 19:21:31.097 R[89443:1009822632] XType: XTFontStaticRegistry is enabled.
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 Apr 10 19:21:31 2023
***********************************************
Number of test functions: 9
Number of errors: 0
Number of failures: 0
1 Test Suite :
ChemmineOB RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
2.827 0.348 3.696
ChemmineOB.Rcheck/ChemmineOB-Ex.timings
| name | user | system | elapsed | |
| canonicalNumbering_OB | 0.000 | 0.001 | 0.001 | |
| convertFormat | 0.000 | 0.000 | 0.001 | |
| convertFormatFile | 0 | 0 | 0 | |
| convertToImage | 0 | 0 | 0 | |
| exactMass_OB | 0.001 | 0.000 | 0.001 | |
| fingerprint_OB | 0 | 0 | 0 | |
| forEachMol | 0.000 | 0.001 | 0.000 | |
| prop_OB | 0 | 0 | 0 | |
| smartsSearch_OB | 0.000 | 0.001 | 0.000 | |