Package: GSEABase

Version: 1.16.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch GSEABase_1.16.0.tar.gz

StartedAt: 2012-01-09 03:35:39 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 03:37:42 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 122.5 seconds

RetCode: 0

Status:  OK

CheckDir: GSEABase.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/GSEABase.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-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 '1.16.0'
* 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 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 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 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	0.83	0.05	0.87
CollectionType-constructors	0.22	0.04	0.27
GSEABase-package	0.25	0.00	0.25
GeneColorSet-class	0.22	0.00	0.22
GeneIdentifierType-class	0.17	0.02	0.18
GeneIdentifierType-constructors	0.11	0.03	0.14
GeneSet-class	0.51	0.00	0.52
GeneSet-methods	0.18	0.00	0.17
GeneSetCollection-class	0.03	0.00	0.03
GeneSetCollection-methods	8.14	0.17	8.88
OBOCollection-class	0.11	0.00	0.11
getOBOCollection	0.04	0.03	0.08
getObjects	0.08	0.00	0.07
goSlim-methods	0.63	0.02	0.80
incidence-methods	0.03	0.00	0.03