BioC 2.12: CHECK report for GSEABase on petty

Package: GSEABase

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GSEABase_1.22.0.tar.gz

StartedAt: 2013-10-08 22:40:53 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:46:29 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 336.8 seconds

RetCode: 0

Status:  OK

CheckDir: GSEABase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GSEABase.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GSEABase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSEABase' version '1.22.0'
* 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 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 ... [22s/22s] 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 ... [35s/35s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
GeneSetCollection-methods 16.995  0.361  17.439
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'unitTests.R' [80s/82s]
 [81s/82s] 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
** testing if installed package can be loaded
* DONE (GSEABase)

name	user	system	elapsed
CollectionType-class	1.489	0.083	1.579
CollectionType-constructors	0.708	0.021	0.744
GSEABase-package	0.358	0.033	0.425
GeneColorSet-class	0.416	0.023	0.449
GeneIdentifierType-class	0.373	0.023	0.399
GeneIdentifierType-constructors	0.973	0.027	1.050
GeneSet-class	0.973	0.035	1.010
GeneSet-methods	0.348	0.022	0.373
GeneSetCollection-class	0.114	0.007	0.121
GeneSetCollection-methods	16.995	0.361	17.439
OBOCollection-class	0.241	0.013	0.255
getOBOCollection	0.171	0.013	0.185
getObjects	0.163	0.017	0.181
goSlim-methods	1.507	0.094	1.618
incidence-methods	0.095	0.011	0.106