Package: GSEABase

Version: 1.13.3

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GSEABase_1.13.3.tar.gz

StartedAt: 2011-02-24 15:55:07 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 15:56:23 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 76.4 seconds

RetCode: 0

Status:  OK

CheckDir: GSEABase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/GSEABase.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GSEABase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSEABase' version '1.13.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GSEABase' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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 ... OK
* 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 ... NOTE
'library' or 'require' call not declared from: Rgraphviz
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'GSEABase' ...
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: AnnotationDbi
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GSEABase)

name	user	system	elapsed
CollectionType-class	0.823	0.028	0.850
CollectionType-constructors	0.267	0.040	0.307
GSEABase-package	0.328	0.009	0.338
GeneColorSet-class	0.272	0.006	0.279
GeneIdentifierType-class	0.198	0.006	0.204
GeneIdentifierType-constructors	0.159	0.005	0.165
GeneSet-class	0.409	0.008	0.417
GeneSet-methods	0.220	0.006	0.226
GeneSetCollection-class	0.031	0.000	0.032
GeneSetCollection-methods	6.806	0.127	6.934
OBOCollection-class	0.127	0.005	0.132
getOBOCollection	0.089	0.004	0.091
getObjects	0.076	0.002	0.078
goSlim-methods	0.843	0.031	0.874
incidence-methods	0.045	0.001	0.045