Package: GSEABase

Version: 1.21.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GSEABase_1.21.6.tar.gz

StartedAt: 2013-03-25 02:57:10 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:01:59 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 289.1 seconds

RetCode: 0

Status:  OK

CheckDir: GSEABase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GSEABase.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.21.6'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'GSEABase' can be installed ... [16s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [29s/29s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
GeneSetCollection-methods 11.297  0.503  11.806
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'unitTests.R' [64s/64s]
 [64s/65s] 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
** help
*** installing help indices
** building package indices
** installing vignettes
   'GSEABase.Rnw' 
** testing if installed package can be loaded
* DONE (GSEABase)

name	user	system	elapsed
CollectionType-class	1.515	0.239	1.756
CollectionType-constructors	0.436	0.042	0.477
GSEABase-package	0.352	0.037	0.394
GeneColorSet-class	0.474	0.050	0.525
GeneIdentifierType-class	0.555	0.055	0.611
GeneIdentifierType-constructors	0.681	0.052	0.734
GeneSet-class	1.000	0.079	1.079
GeneSet-methods	0.358	0.042	0.400
GeneSetCollection-class	0.159	0.026	0.186
GeneSetCollection-methods	11.297	0.503	11.806
OBOCollection-class	0.128	0.017	0.145
getOBOCollection	0.086	0.011	0.096
getObjects	0.082	0.020	0.103
goSlim-methods	0.930	0.079	1.008
incidence-methods	0.044	0.011	0.054