Package: yaqcaffy

Version: 1.11.4

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings yaqcaffy_1.11.4.tar.gz

StartedAt: 2011-02-24 20:13:46 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 20:17:16 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 209.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: yaqcaffy.Rcheck

Warnings: 1

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/yaqcaffy.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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
  'E:/biocbld/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	0	0
getAllInt	15.67	0.40	16.14
getBioProbes	1.24	0.00	1.26
getOutliers	45.17	0.65	46.89
getQCRatios	9.98	0.21	10.22
getRatioProbes	1.39	0.05	1.44
getSpikeProbes	1.41	0.02	1.42
probeSelectionInterface	0	0	0
reprodPlot	0	0	0
yaqc.affy	9.72	0.23	9.96
yaqc.plot	9.53	0.17	9.71
yaqc.summary	10.11	0.17	10.30