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: 2011-03-17 17:47:45 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:51:23 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 218.7 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) (2011-03-06 r54683)
* 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 '1.11.4'
* 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 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 ... 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	0.002	0.000	0.002
getAllInt	13.987	0.521	14.516
getBioProbes	1.116	0.019	1.134
getOutliers	43.719	1.381	45.359
getQCRatios	9.662	0.586	10.248
getRatioProbes	1.473	0.026	1.500
getSpikeProbes	1.498	0.022	1.521
probeSelectionInterface	0.000	0.000	0.001
reprodPlot	0	0	0
yaqc.affy	9.743	0.583	10.326
yaqc.plot	10.107	0.601	10.767
yaqc.summary	9.739	0.503	10.242