BioC 3.3: CHECK report for npGSEA on morelia

Package: npGSEA

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings npGSEA_1.7.0.tar.gz

StartedAt: 2015-10-22 09:05:51 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 09:07:09 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 78.2 seconds

RetCode: 0

Status:  OK

CheckDir: npGSEA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings npGSEA_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/npGSEA.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘npGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘npGSEA’ version ‘1.7.0’
* 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 ‘npGSEA’ can be installed ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘npGSEA’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (npGSEA)

name	user	system	elapsed
DF-methods	0.019	0.000	0.020
alphaValue-methods	0.009	0.001	0.009
betaHats-methods	0.006	0.000	0.007
betaStat-methods	0.006	0.000	0.006
betaValue-methods	0.006	0.001	0.006
chiSqStat-methods	0.010	0.002	0.013
geneSetName-methods	0.006	0.001	0.007
getIncidence	0.004	0.001	0.005
npGSEA	0.006	0.001	0.006
npGSEAPlot-methods	0.005	0.001	0.006
npGSEAResultBeta-class	0.001	0.001	0.001
npGSEAResultBetaCollection-class	0.001	0.000	0.001
npGSEAResultChiSq-class	0.000	0.000	0.001
npGSEAResultChiSqCollection-class	0.001	0.000	0.001
npGSEAResultNorm-class	0.000	0.000	0.001
npGSEAResultNormCollection-class	0.001	0.000	0.000
pLeft-methods	0.006	0.001	0.007
pRight-methods	0.008	0.001	0.008
pTwoSided-methods	0.006	0.000	0.005
pValues-methods	0.005	0.000	0.006
show-methods	0.005	0.001	0.005
sigmaSq-methods	0.006	0.000	0.006
stat-methods	0.005	0.000	0.006
xSet-methods	0.006	0.001	0.006
zStat-methods	0.005	0.000	0.006