BioC 3.3: CHECK report for AnnotationDbi on morelia

Package: AnnotationDbi

Version: 1.33.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationDbi_1.33.0.tar.gz

StartedAt: 2015-10-22 03:23:24 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 03:31:15 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 470.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: AnnotationDbi.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationDbi_1.33.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/AnnotationDbi.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.33.0’
* 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 ‘AnnotationDbi’ can be installed ... [6s/15s] OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    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’
createORGANISMSeeds: no visible global function definition for
  ‘makeAnnDbMapSeeds’
makeGOGraph: no visible binding for global variable ‘GOBPPARENTS’
makeGOGraph: no visible binding for global variable ‘GOMFPARENTS’
makeGOGraph: no visible binding for global variable ‘GOCCPARENTS’
makeGOGraph: no visible global function definition for ‘ftM2graphNEL’
Undefined global functions or variables:
  GOBPPARENTS GOCCPARENTS GOMFPARENTS ftM2graphNEL makeAnnDbMapSeeds
  pkgName
* checking Rd files ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [165s/311s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
AnnDbPkg-checker          114.782  5.123 262.363
Bimap-direction             6.518  0.054   6.571
InparanoidColsAndKeytypes   5.676  0.623   8.968
GOFrame                     5.353  0.600   5.990
* checking for unstated dependencies in ‘tests’ ... WARNING
'library' or 'require' call not declared from: ‘org.testing.db’
* checking tests ...
  Running ‘AnnotationDbi_unit_tests.R’ [65s/82s]
 [66s/82s] 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/AnnotationDbi.Rcheck/00check.log’
for details.

* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘toString’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AnnotationDbi)

name	user	system	elapsed
AnnDbObj-class	0.384	0.015	0.441
AnnDbPkg-checker	114.782	5.123	262.363
AnnotationDb-class	1.215	0.013	1.267
Bimap-direction	6.518	0.054	6.571
Bimap-envirAPI	1.893	0.243	2.135
Bimap-keys	1.723	0.012	1.735
Bimap-toTable	3.881	0.040	4.010
Bimap	3.552	0.004	3.557
BimapFiltering	0.639	0.001	0.640
BimapFormatting	1.738	0.004	1.743
GOColsAndKeytypes	0.515	0.010	0.525
GOFrame	5.353	0.600	5.990
GOTerms-class	0.004	0.000	0.004
InparanoidColsAndKeytypes	5.676	0.623	8.968
KEGGFrame	0.907	0.002	0.909
colsAndKeytypes	0.722	0.012	0.789
createSimpleBimap	0.553	0.002	0.556
inpIDMapper	0.001	0.000	0.001
makeGOGraph	1.020	0.006	1.026
make_eg_to_go_map	0.661	0.003	0.665
print.probetable	3.728	0.212	3.940
toSQLStringSet	0.002	0.000	0.002
unlist2	0.596	0.004	0.599