BioC 3.0: CHECK report for GSEABase on perceval

Package: GSEABase

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GSEABase_1.28.0.tar.gz

StartedAt: 2015-04-10 02:31:15 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:35:47 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 272.7 seconds

RetCode: 0

Status:  OK

CheckDir: GSEABase.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GSEABase_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GSEABase.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSEABase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEABase’ version ‘1.28.0’
* 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 ‘GSEABase’ can be installed ... [20s/26s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.GSC_genes_helper: no visible global function definition for
  ‘mappedLkeys’
.GSC_genes_helper: no visible global function definition for
  ‘mappedRkeys’
.GSC_Pfam_helper: no visible global function definition for ‘select’
GeneSetCollection,character-AnnotationIdentifier-GOCollection: no
  visible global function definition for ‘mappedLkeys’
GeneSetCollection,character-AnnotationIdentifier-GOCollection: no
  visible global function definition for ‘toTable’
GeneSetCollection,GOAllFrame-missing-GOCollection: no visible global
  function definition for ‘getGOFrameData’
GeneSetCollection,KEGGFrame-missing-KEGGCollection: no visible global
  function definition for ‘getKEGGFrameData’
* 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 ... [26s/26s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
GeneSetCollection-methods 12.431  0.341  12.777
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘unitTests.R’ [63s/63s]
 [64s/64s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/GSEABase.Rcheck/00check.log’
for details.

* installing *source* package ‘GSEABase’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GSEABase)

name	user	system	elapsed
CollectionType-class	1.073	0.061	1.136
CollectionType-constructors	0.281	0.019	0.301
GSEABase-package	0.260	0.024	0.291
GeneColorSet-class	0.263	0.019	0.282
GeneIdentifierType-class	0.595	0.023	0.632
GeneIdentifierType-constructors	0.381	0.034	0.451
GeneSet-class	0.411	0.024	0.449
GeneSet-methods	0.228	0.016	0.245
GeneSetCollection-class	0.024	0.001	0.025
GeneSetCollection-methods	12.431	0.341	12.777
OBOCollection-class	0.158	0.004	0.162
getOBOCollection	0.137	0.009	0.147
getObjects	0.057	0.003	0.072
goSlim-methods	1.123	0.067	1.226
incidence-methods	0.067	0.003	0.070