AnnotationDbi using generics test result

check.log

R --no-site-file --no-environ --no-save --no-restore CMD check '/tmp/RtmprefbcS/AnnotationDbi_1.33.3.tar.gz' --as-cran  \
  --timings

* using log directory ‘/tmp/RtmprefbcS/AnnotationDbi.Rcheck’
* using R Under development (unstable) (2015-08-17 r69096)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.33.3’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AnnotationDbi’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R         4.0Mb
    extdata   6.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘utils’ ‘stats4’ ‘BiocGenerics’ ‘Biobase’ ‘IRanges’ ‘DBI’ ‘RSQLite’
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
'library' or 'require' calls in package code:
  ‘GO.db’ ‘KEGG.db’ ‘RSQLite’ ‘graph’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘createAnnDbBimap’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotMessage: no visible binding for global variable ‘pkgName’
  (/tmp/RtmprefbcS/AnnotationDbi.Rcheck/00_pkg_src/AnnotationDbi/R/createAnnObjs-utils.R:240-300)
createORGANISMSeeds: no visible global function definition for
  ‘makeAnnDbMapSeeds’
  (/tmp/RtmprefbcS/AnnotationDbi.Rcheck/00_pkg_src/AnnotationDbi/R/createAnnObjs.ORGANISM_DB.R:140)
makeGOGraph: no visible binding for global variable ‘GOBPPARENTS’
  (/tmp/RtmprefbcS/AnnotationDbi.Rcheck/00_pkg_src/AnnotationDbi/R/GOTerms.R:341-345)
makeGOGraph: no visible binding for global variable ‘GOMFPARENTS’
  (/tmp/RtmprefbcS/AnnotationDbi.Rcheck/00_pkg_src/AnnotationDbi/R/GOTerms.R:341-345)
makeGOGraph: no visible binding for global variable ‘GOCCPARENTS’
  (/tmp/RtmprefbcS/AnnotationDbi.Rcheck/00_pkg_src/AnnotationDbi/R/GOTerms.R:341-345)
makeGOGraph: no visible global function definition for ‘ftM2graphNEL’
  (/tmp/RtmprefbcS/AnnotationDbi.Rcheck/00_pkg_src/AnnotationDbi/R/GOTerms.R:346)
Undefined global functions or variables:
  GOBPPARENTS GOCCPARENTS GOMFPARENTS ftM2graphNEL makeAnnDbMapSeeds
  pkgName
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'inpIDMapper.Rd':
  \examples lines wider than 100 characters:
       YeastUPSingles = inpIDMapper(ids, "HOMSA", "SACCE", destIDType="UNIPROT", keepMultDestIDMatches = FALSE)

These lines will be truncated in the PDF manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
AnnDbPkg-checker          123.752  0.744 124.545
Bimap-direction             9.002  0.008   9.012
InparanoidColsAndKeytypes   5.576  0.068   5.650
Bimap-toTable               5.579  0.024   5.604
GOFrame                     5.435  0.160   5.602
* checking for unstated dependencies in ‘tests’ ... WARNING
'library' or 'require' call not declared from: ‘org.testing.db’
* checking tests ...
  Running ‘AnnotationDbi_unit_tests.R’ [71s/71s]
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs