Package: GSEABase

Version: 1.16.1

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GSEABase_1.16.1.tar.gz

StartedAt: 2012-03-24 01:45:02 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:48:06 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 184.2 seconds

RetCode: 0

Status:  OK

CheckDir: GSEABase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/GSEABase.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.16.1'
* 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 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 sizes of PDF files under 'inst/doc' ... OK
* 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
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
** 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	1.171	0.065	1.249
CollectionType-constructors	0.320	0.082	0.409
GSEABase-package	0.322	0.016	0.341
GeneColorSet-class	0.338	0.012	0.352
GeneIdentifierType-class	0.279	0.013	0.300
GeneIdentifierType-constructors	0.234	0.012	0.245
GeneSet-class	0.695	0.022	0.718
GeneSet-methods	0.293	0.015	0.310
GeneSetCollection-class	0.029	0.000	0.030
GeneSetCollection-methods	9.432	0.374	9.883
OBOCollection-class	0.145	0.006	0.156
getOBOCollection	0.103	0.011	0.114
getObjects	0.106	0.004	0.109
goSlim-methods	1.014	0.081	1.133
incidence-methods	0.051	0.002	0.053