Package: yaqcaffy

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch yaqcaffy_1.13.0.tar.gz

StartedAt: 2011-06-22 05:52:55 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 05:57:52 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 297.8 seconds

RetCode: 0

Status:  OK

CheckDir: yaqcaffy.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/yaqcaffy.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘yaqcaffy/DESCRIPTION’ ... OK
* this is package ‘yaqcaffy’ version ‘1.13.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘yaqcaffy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 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 ‘yaqcaffy’ ...
** R
** inst
** preparing package for lazy loading
Loading required package: affy
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: genefilter
Loading required package: gcrma
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 ...
*** tangling vignette sources ...
   ‘yaqcaffy.Rnw’ 
** testing if installed package can be loaded

* DONE (yaqcaffy)

name	user	system	elapsed
YaqcControlProbes-class	0.003	0.001	0.004
getAllInt	20.093	1.208	21.414
getBioProbes	1.706	0.057	1.769
getOutliers	61.559	2.729	64.531
getQCRatios	13.951	1.113	15.098
getRatioProbes	2.085	0.059	2.144
getSpikeProbes	2.136	0.056	2.193
probeSelectionInterface	0.000	0.000	0.001
reprodPlot	0	0	0
yaqc.affy	13.236	0.990	14.234
yaqc.plot	13.568	0.985	14.561