Package: GSEABase

Version: 1.15.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch GSEABase_1.15.0.tar.gz

StartedAt: 2011-07-07 02:14:28 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 02:16:02 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 93.8 seconds

RetCode: 0

Status:  OK

CheckDir: GSEABase.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/GSEABase.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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	0.83	0.03	0.88
CollectionType-constructors	0.19	0.03	0.50
GSEABase-package	0.28	0.02	0.67
GeneColorSet-class	0.25	0.01	0.27
GeneIdentifierType-class	0.17	0.02	0.19
GeneIdentifierType-constructors	0.16	0.00	0.15
GeneSet-class	0.4	0.0	0.5
GeneSet-methods	0.18	0.01	0.28
GeneSetCollection-class	0.13	0.00	0.13
GeneSetCollection-methods	7.55	0.04	7.75
OBOCollection-class	0.12	0.00	0.12
getOBOCollection	0.08	0.00	0.08
getObjects	0.08	0.00	0.08
goSlim-methods	0.67	0.03	0.77
incidence-methods	0.03	0.00	0.03