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###
### Running command:
###
### rm -rf ChemmineOB.buildbin-libdir ChemmineOB.Rcheck && mkdir ChemmineOB.buildbin-libdir ChemmineOB.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChemmineOB.buildbin-libdir ChemmineOB_1.7.1.tar.gz >ChemmineOB.Rcheck\00install.out 2>&1 && cp ChemmineOB.Rcheck\00install.out ChemmineOB-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ChemmineOB.buildbin-libdir --install="check:ChemmineOB-install.out" --force-multiarch --no-vignettes --timings ChemmineOB_1.7.1.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/ChemmineOB.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChemmineOB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChemmineOB' version '1.7.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'ChemmineOB' can be installed ... OK
* checking installed package size ... NOTE
installed size is 16.4Mb
sub-directories of 1Mb or more:
R 1.3Mb
libs 12.9Mb
openbabel_data 2.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'ChemmineR'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
'BiocGenerics' 'Rcpp'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
copyToC: no visible global function definition for 'RSWIG_createNewRef'
copyToC,OpenBabel::CharPtrLess: no visible global function definition
for 'RSWIG_createNewRef'
copyToC,OpenBabel::DoubleType: no visible global function definition
for 'RSWIG_createNewRef'
copyToC,OpenBabel::FptIndexHeader: no visible global function
definition for 'RSWIG_createNewRef'
copyToC,OpenBabel::LineSearchType: no visible global function
definition for 'RSWIG_createNewRef'
copyToC,std::pair<(unsigned int,unsigned int)>: no visible global
function definition for 'RSWIG_createNewRef'
copyToC,stringp: no visible global function definition for
'RSWIG_createNewRef'
delete,_p_OpenBabel__AliasData: no visible global function definition
for 'delete_OpenBabel__AliasData'
delete,_p_OpenBabel__CharPtrLess: no visible global function definition
for 'delete_OpenBabel__CharPtrLess'
delete,_p_OpenBabel__DoubleType: no visible global function definition
for 'delete_OpenBabel__DoubleType'
delete,_p_OpenBabel__FastSearch: no visible global function definition
for 'delete_OpenBabel__FastSearch'
delete,_p_OpenBabel__FastSearchIndexer: no visible global function
definition for 'delete_OpenBabel__FastSearchIndexer'
delete,_p_OpenBabel__FptIndexHeader: no visible global function
definition for 'delete_OpenBabel__FptIndexHeader'
delete,_p_OpenBabel__LineSearchType: no visible global function
definition for 'delete_OpenBabel__LineSearchType'
delete,_p_OpenBabel__OBAngle: no visible global function definition for
'delete_OpenBabel__OBAngle'
delete,_p_OpenBabel__OBAngleData: no visible global function definition
for 'delete_OpenBabel__OBAngleData'
delete,_p_OpenBabel__OBAromaticTyper: no visible global function
definition for 'delete_OpenBabel__OBAromaticTyper'
delete,_p_OpenBabel__OBAtom: no visible global function definition for
'delete_OpenBabel__OBAtom'
delete,_p_OpenBabel__OBAtomAtomIter: no visible global function
definition for 'delete_OpenBabel__OBAtomAtomIter'
delete,_p_OpenBabel__OBAtomBondIter: no visible global function
definition for 'delete_OpenBabel__OBAtomBondIter'
delete,_p_OpenBabel__OBAtomClassData: no visible global function
definition for 'delete_OpenBabel__OBAtomClassData'
delete,_p_OpenBabel__OBAtomTyper: no visible global function definition
for 'delete_OpenBabel__OBAtomTyper'
delete,_p_OpenBabel__OBBase: no visible global function definition for
'delete_OpenBabel__OBBase'
delete,_p_OpenBabel__OBBitVec: no visible global function definition
for 'delete_OpenBabel__OBBitVec'
delete,_p_OpenBabel__OBBond: no visible global function definition for
'delete_OpenBabel__OBBond'
delete,_p_OpenBabel__OBBuilder: no visible global function definition
for 'delete_OpenBabel__OBBuilder'
delete,_p_OpenBabel__OBChainsParser: no visible global function
definition for 'delete_OpenBabel__OBChainsParser'
delete,_p_OpenBabel__OBChiralData: no visible global function
definition for 'delete_OpenBabel__OBChiralData'
delete,_p_OpenBabel__OBCommentData: no visible global function
definition for 'delete_OpenBabel__OBCommentData'
delete,_p_OpenBabel__OBConformerData: no visible global function
definition for 'delete_OpenBabel__OBConformerData'
delete,_p_OpenBabel__OBConversion: no visible global function
definition for 'delete_OpenBabel__OBConversion'
delete,_p_OpenBabel__OBDOSData: no visible global function definition
for 'delete_OpenBabel__OBDOSData'
delete,_p_OpenBabel__OBDescriptor: no visible global function
definition for 'delete_OpenBabel__OBDescriptor'
delete,_p_OpenBabel__OBElectronicTransitionData: no visible global
function definition for
'delete_OpenBabel__OBElectronicTransitionData'
delete,_p_OpenBabel__OBElement: no visible global function definition
for 'delete_OpenBabel__OBElement'
delete,_p_OpenBabel__OBElementTable: no visible global function
definition for 'delete_OpenBabel__OBElementTable'
delete,_p_OpenBabel__OBError: no visible global function definition for
'delete_OpenBabel__OBError'
delete,_p_OpenBabel__OBExternalBond: no visible global function
definition for 'delete_OpenBabel__OBExternalBond'
delete,_p_OpenBabel__OBExternalBondData: no visible global function
definition for 'delete_OpenBabel__OBExternalBondData'
delete,_p_OpenBabel__OBFFCalculation2: no visible global function
definition for 'delete_OpenBabel__OBFFCalculation2'
delete,_p_OpenBabel__OBFFCalculation3: no visible global function
definition for 'delete_OpenBabel__OBFFCalculation3'
delete,_p_OpenBabel__OBFFCalculation4: no visible global function
definition for 'delete_OpenBabel__OBFFCalculation4'
delete,_p_OpenBabel__OBFFConstraint: no visible global function
definition for 'delete_OpenBabel__OBFFConstraint'
delete,_p_OpenBabel__OBFFConstraints: no visible global function
definition for 'delete_OpenBabel__OBFFConstraints'
delete,_p_OpenBabel__OBFFParameter: no visible global function
definition for 'delete_OpenBabel__OBFFParameter'
delete,_p_OpenBabel__OBFingerprint: no visible global function
definition for 'delete_OpenBabel__OBFingerprint'
delete,_p_OpenBabel__OBForceField: no visible global function
definition for 'delete_OpenBabel__OBForceField'
delete,_p_OpenBabel__OBFormat: no visible global function definition
for 'delete_OpenBabel__OBFormat'
delete,_p_OpenBabel__OBGenericData: no visible global function
definition for 'delete_OpenBabel__OBGenericData'
delete,_p_OpenBabel__OBGlobalDataBase: no visible global function
definition for 'delete_OpenBabel__OBGlobalDataBase'
delete,_p_OpenBabel__OBGridData: no visible global function definition
for 'delete_OpenBabel__OBGridData'
delete,_p_OpenBabel__OBInternalCoord: no visible global function
definition for 'delete_OpenBabel__OBInternalCoord'
delete,_p_OpenBabel__OBIsotopeTable: no visible global function
definition for 'delete_OpenBabel__OBIsotopeTable'
delete,_p_OpenBabel__OBMatrixData: no visible global function
definition for 'delete_OpenBabel__OBMatrixData'
delete,_p_OpenBabel__OBMessageHandler: no visible global function
definition for 'delete_OpenBabel__OBMessageHandler'
delete,_p_OpenBabel__OBMol: no visible global function definition for
'delete_OpenBabel__OBMol'
delete,_p_OpenBabel__OBMolAngleIter: no visible global function
definition for 'delete_OpenBabel__OBMolAngleIter'
delete,_p_OpenBabel__OBMolAtomBFSIter: no visible global function
definition for 'delete_OpenBabel__OBMolAtomBFSIter'
delete,_p_OpenBabel__OBMolAtomDFSIter: no visible global function
definition for 'delete_OpenBabel__OBMolAtomDFSIter'
delete,_p_OpenBabel__OBMolAtomIter: no visible global function
definition for 'delete_OpenBabel__OBMolAtomIter'
delete,_p_OpenBabel__OBMolBondBFSIter: no visible global function
definition for 'delete_OpenBabel__OBMolBondBFSIter'
delete,_p_OpenBabel__OBMolBondIter: no visible global function
definition for 'delete_OpenBabel__OBMolBondIter'
delete,_p_OpenBabel__OBMolPairIter: no visible global function
definition for 'delete_OpenBabel__OBMolPairIter'
delete,_p_OpenBabel__OBMolRingIter: no visible global function
definition for 'delete_OpenBabel__OBMolRingIter'
delete,_p_OpenBabel__OBMolTorsionIter: no visible global function
definition for 'delete_OpenBabel__OBMolTorsionIter'
delete,_p_OpenBabel__OBOp: no visible global function definition for
'delete_OpenBabel__OBOp'
delete,_p_OpenBabel__OBOrbital: no visible global function definition
for 'delete_OpenBabel__OBOrbital'
delete,_p_OpenBabel__OBOrbitalData: no visible global function
definition for 'delete_OpenBabel__OBOrbitalData'
delete,_p_OpenBabel__OBPairData: no visible global function definition
for 'delete_OpenBabel__OBPairData'
delete,_p_OpenBabel__OBPlugin: no visible global function definition
for 'delete_OpenBabel__OBPlugin'
delete,_p_OpenBabel__OBRTree: no visible global function definition for
'delete_OpenBabel__OBRTree'
delete,_p_OpenBabel__OBRandom: no visible global function definition
for 'delete_OpenBabel__OBRandom'
delete,_p_OpenBabel__OBResidue: no visible global function definition
for 'delete_OpenBabel__OBResidue'
delete,_p_OpenBabel__OBResidueAtomIter: no visible global function
definition for 'delete_OpenBabel__OBResidueAtomIter'
delete,_p_OpenBabel__OBResidueData: no visible global function
definition for 'delete_OpenBabel__OBResidueData'
delete,_p_OpenBabel__OBResidueIter: no visible global function
definition for 'delete_OpenBabel__OBResidueIter'
delete,_p_OpenBabel__OBRing: no visible global function definition for
'delete_OpenBabel__OBRing'
delete,_p_OpenBabel__OBRingData: no visible global function definition
for 'delete_OpenBabel__OBRingData'
delete,_p_OpenBabel__OBRingSearch: no visible global function
definition for 'delete_OpenBabel__OBRingSearch'
delete,_p_OpenBabel__OBRingTyper: no visible global function definition
for 'delete_OpenBabel__OBRingTyper'
delete,_p_OpenBabel__OBRotationData: no visible global function
definition for 'delete_OpenBabel__OBRotationData'
delete,_p_OpenBabel__OBSSMatch: no visible global function definition
for 'delete_OpenBabel__OBSSMatch'
delete,_p_OpenBabel__OBSerialNums: no visible global function
definition for 'delete_OpenBabel__OBSerialNums'
delete,_p_OpenBabel__OBSetData: no visible global function definition
for 'delete_OpenBabel__OBSetData'
delete,_p_OpenBabel__OBSmartsMatcher: no visible global function
definition for 'delete_OpenBabel__OBSmartsMatcher'
delete,_p_OpenBabel__OBSmartsPattern: no visible global function
definition for 'delete_OpenBabel__OBSmartsPattern'
delete,_p_OpenBabel__OBSqrtTbl: no visible global function definition
for 'delete_OpenBabel__OBSqrtTbl'
delete,_p_OpenBabel__OBStopwatch: no visible global function definition
for 'delete_OpenBabel__OBStopwatch'
delete,_p_OpenBabel__OBSymmetryData: no visible global function
definition for 'delete_OpenBabel__OBSymmetryData'
delete,_p_OpenBabel__OBTorsion: no visible global function definition
for 'delete_OpenBabel__OBTorsion'
delete,_p_OpenBabel__OBTorsionData: no visible global function
definition for 'delete_OpenBabel__OBTorsionData'
delete,_p_OpenBabel__OBTypeTable: no visible global function definition
for 'delete_OpenBabel__OBTypeTable'
delete,_p_OpenBabel__OBUnitCell: no visible global function definition
for 'delete_OpenBabel__OBUnitCell'
delete,_p_OpenBabel__OBVectorData: no visible global function
definition for 'delete_OpenBabel__OBVectorData'
delete,_p_OpenBabel__OBVibrationData: no visible global function
definition for 'delete_OpenBabel__OBVibrationData'
delete,_p_OpenBabel__OBVirtualBond: no visible global function
definition for 'delete_OpenBabel__OBVirtualBond'
delete,_p_OpenBabel__SpaceGroup: no visible global function definition
for 'delete_OpenBabel__SpaceGroup'
delete,_p_OpenBabel__matrix3x3: no visible global function definition
for 'delete_OpenBabel__matrix3x3'
delete,_p_OpenBabel__obLogBuf: no visible global function definition
for 'delete_OpenBabel__obLogBuf'
delete,_p_OpenBabel__transform3d: no visible global function definition
for 'delete_OpenBabel__transform3d'
delete,_p_OpenBabel__vector3: no visible global function definition for
'delete_OpenBabel__vector3'
delete,_p_std__binary_functionT_char_const_p_char_const_p_bool_t: no
visible global function definition for
'delete_std__binary_functionT_char_const_p_char_const_p_bool_t'
delete,_p_std__pairT_unsigned_int_unsigned_int_t: no visible global
function definition for
'delete_std__pairT_unsigned_int_unsigned_int_t'
delete,_p_std__stringbuf: no visible global function definition for
'delete_std__stringbuf'
delete,_p_std__vectorT_OpenBabel__OBBond_std__allocatorT_OpenBabel__OBBond_t_t:
no visible global function definition for
'delete_std__vectorT_OpenBabel__OBBond_std__allocatorT_OpenBabel__OBBond_t_t'
delete,_p_std__vectorT_OpenBabel__OBGenericData_p_std__allocatorT_OpenBabel__OBGenericData_p_t_t:
no visible global function definition for
'delete_std__vectorT_OpenBabel__OBGenericData_p_std__allocatorT_OpenBabel__OBGenericData_p_t_t'
delete,_p_std__vectorT_OpenBabel__OBInternalCoord_p_std__allocatorT_OpenBabel__OBInternalCoord_p_t_t:
no visible global function definition for
'delete_std__vectorT_OpenBabel__OBInternalCoord_p_std__allocatorT_OpenBabel__OBInternalCoord_p_t_t'
delete,_p_std__vectorT_OpenBabel__OBMol_std__allocatorT_OpenBabel__OBMol_t_t:
no visible global function definition for
'delete_std__vectorT_OpenBabel__OBMol_std__allocatorT_OpenBabel__OBMol_t_t'
delete,_p_std__vectorT_OpenBabel__OBResidue_std__allocatorT_OpenBabel__OBResidue_t_t:
no visible global function definition for
'delete_std__vectorT_OpenBabel__OBResidue_std__allocatorT_OpenBabel__OBResidue_t_t'
delete,_p_std__vectorT_OpenBabel__OBRing_p_std__allocatorT_OpenBabel__OBRing_p_t_t:
no visible global function definition for
'delete_std__vectorT_OpenBabel__OBRing_p_std__allocatorT_OpenBabel__OBRing_p_t_t'
delete,_p_std__vectorT_OpenBabel__OBRing_std__allocatorT_OpenBabel__OBRing_t_t:
no visible global function definition for
'delete_std__vectorT_OpenBabel__OBRing_std__allocatorT_OpenBabel__OBRing_t_t'
delete,_p_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t:
no visible global function definition for
'delete_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t'
delete,_p_std__vectorT_double_std__allocatorT_double_t_t: no visible
global function definition for
'delete_std__vectorT_double_std__allocatorT_double_t_t'
delete,_p_std__vectorT_int_std__allocatorT_int_t_t: no visible global
function definition for
'delete_std__vectorT_int_std__allocatorT_int_t_t'
delete,_p_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t:
no visible global function definition for
'delete_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t'
delete,_p_std__vectorT_std__string_std__allocatorT_std__string_t_t: no
visible global function definition for
'delete_std__vectorT_std__string_std__allocatorT_std__string_t_t'
delete,_p_std__vectorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_std__allocatorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_t_t:
no visible global function definition for
'delete_std__vectorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_std__allocatorT_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__vector3_t_t_t_t'
delete,_p_std__vectorT_std__vectorT_int_std__allocatorT_int_t_t_std__allocatorT_std__vectorT_int_std__allocatorT_int_t_t_t_t:
no visible global function definition for
'delete_std__vectorT_std__vectorT_int_std__allocatorT_int_t_t_std__allocatorT_std__vectorT_int_std__allocatorT_int_t_t_t_t'
delete,_p_std__vectorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_std__allocatorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_t_t:
no visible global function definition for
'delete_std__vectorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_std__allocatorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_t_t'
delete,_p_std__vectorT_unsigned_int_std__allocatorT_unsigned_int_t_t:
no visible global function definition for
'delete_std__vectorT_unsigned_int_std__allocatorT_unsigned_int_t_t'
* checking Rd files ... NOTE
prepare_Rd: canonicalNumbering_OB.Rd:30-32: Dropping empty section \note
prepare_Rd: forEachMol.Rd:48-50: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars.in
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.2-bioc/meat/ChemmineOB.buildbin-libdir/ChemmineOB/libs/i386/ChemmineOB.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Found 'rand', possibly from 'rand' (C)
Found 'srand', possibly from 'srand' (C)
File 'D:/biocbld/bbs-3.2-bioc/meat/ChemmineOB.buildbin-libdir/ChemmineOB/libs/x64/ChemmineOB.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Found 'rand', possibly from 'rand' (C)
Found 'srand', possibly from 'srand' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [5s] OK
** running examples for arch 'x64' ... [5s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [5s]
[5s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [5s]
[6s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 6 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/ChemmineOB.Rcheck/00check.log'
for details.
