BioC 2.12: CHECK report for yaqcaffy on petty

Package: yaqcaffy

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch yaqcaffy_1.20.0.tar.gz

StartedAt: 2013-10-09 00:10:42 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:15:20 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 278.0 seconds

RetCode: 0

Status:  OK

CheckDir: yaqcaffy.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/yaqcaffy.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 'yaqcaffy/DESCRIPTION' ... OK
* this is package 'yaqcaffy' version '1.20.0'
* 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 'yaqcaffy' can be installed ... [21s/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 ... [98s/98s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOutliers 40.768  1.634  42.571
getAllInt   16.271  0.608  16.944
getQCRatios  8.903  0.647   9.550
yaqc.affy    8.720  0.772   9.493
yaqc.plot    8.367  0.571   8.937
* 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 'yaqcaffy' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'yaqcaffy'
Creating a generic function for 'merge' from package 'base' in package 'yaqcaffy'
Creating a generic function for 'identical' from package 'base' in package 'yaqcaffy'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (yaqcaffy)

name	user	system	elapsed
YaqcControlProbes-class	0.009	0.003	0.012
getAllInt	16.271	0.608	16.944
getBioProbes	0.698	0.027	0.725
getOutliers	40.768	1.634	42.571
getQCRatios	8.903	0.647	9.550
getRatioProbes	1.047	0.075	1.204
getSpikeProbes	1.015	0.036	1.068
probeSelectionInterface	0.003	0.003	0.006
reprodPlot	0.002	0.004	0.006
yaqc.affy	8.720	0.772	9.493
yaqc.plot	8.367	0.571	8.937