Package: yaqcaffy

Version: 1.11.4

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch yaqcaffy_1.11.4.tar.gz

StartedAt: 2011-02-24 21:48:56 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 21:53:38 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 282.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: yaqcaffy.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/yaqcaffy.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.11.4’
* 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 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 ... WARNING
Undocumented S4 methods:
  generic 'merge' and siglist 'YAQCStats,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/Users/biocbuild/bbs-2.8-bioc/meat/yaqcaffy.Rcheck/00check.log’
for details

* 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 new generic function for "summary" in "yaqcaffy"
Creating a new generic function for "merge" in "yaqcaffy"
Creating a new generic function for "identical" in "yaqcaffy"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (yaqcaffy)

name	user	system	elapsed
YaqcControlProbes-class	0.004	0.000	0.004
getAllInt	19.632	1.176	20.875
getBioProbes	1.636	0.050	1.688
getOutliers	62.231	2.698	65.082
getQCRatios	13.800	1.063	14.878
getRatioProbes	2.144	0.067	2.215
getSpikeProbes	2.089	0.055	2.146
probeSelectionInterface	0.000	0.000	0.001
reprodPlot	0.000	0.001	0.001
yaqc.affy	14.280	1.126	15.428
yaqc.plot	13.974	1.020	15.012
yaqc.summary	14.190	0.989	15.188