Package: yaqcaffy

Version: 1.17.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch yaqcaffy_1.17.1.tar.gz

StartedAt: 2012-06-21 04:22:42 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 04:27:43 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 300.9 seconds

RetCode: 0

Status:  OK

CheckDir: yaqcaffy.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/yaqcaffy.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'yaqcaffy/DESCRIPTION' ... OK
* this is package 'yaqcaffy' version '1.17.1'
* 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 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 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 ... 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
No methods found in "Biobase" for requests: geneNames
No methods found in "Biobase" for requests: geneNames
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
   'yaqcaffy.Rnw' 
** testing if installed package can be loaded
No methods found in "Biobase" for requests: geneNames
No methods found in "Biobase" for requests: geneNames

* DONE (yaqcaffy)

name	user	system	elapsed
YaqcControlProbes-class	0.003	0.001	0.004
getAllInt	20.088	1.047	21.274
getBioProbes	1.005	0.045	1.051
getOutliers	57.509	2.160	59.891
getQCRatios	13.486	0.839	14.341
getRatioProbes	1.462	0.064	1.527
getSpikeProbes	1.510	0.062	1.572
probeSelectionInterface	0	0	0
reprodPlot	0.000	0.001	0.000
yaqc.affy	13.449	0.831	14.324
yaqc.plot	13.947	0.840	14.834