Package: GSEABase

Version: 1.15.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings GSEABase_1.15.0.tar.gz

StartedAt: 2011-05-09 12:49:44 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 12:51:14 -0700 (Mon, 09 May 2011)

EllapsedTime: 90.7 seconds

RetCode: 0

Status:  OK

CheckDir: GSEABase.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GSEABase.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.15.0’
* 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 installed package size ... 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 for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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 ...
*** tangling vignette sources ...
   ‘GSEABase.Rnw’ 
** testing if installed package can be loaded

* DONE (GSEABase)

name	user	system	elapsed
CollectionType-class	0.804	0.040	0.849
CollectionType-constructors	0.336	0.016	0.361
GSEABase-package	0.212	0.012	0.225
GeneColorSet-class	0.228	0.008	0.237
GeneIdentifierType-class	0.152	0.004	0.156
GeneIdentifierType-constructors	0.128	0.008	0.133
GeneSet-class	0.356	0.000	0.358
GeneSet-methods	0.176	0.004	0.181
GeneSetCollection-class	0.028	0.000	0.030
GeneSetCollection-methods	8.980	0.084	9.164
OBOCollection-class	0.112	0.000	0.116
getOBOCollection	0.064	0.000	0.067
getObjects	0.080	0.000	0.082
goSlim-methods	0.588	0.020	0.630
incidence-methods	0.040	0.000	0.041