Package: yaqcaffy

Version: 1.11.4

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

StartedAt: 2011-02-24 22:15:21 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 22:18:49 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 207.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: yaqcaffy.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/yaqcaffy.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-pc-mingw32 (64-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
  'D:/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	15.55	0.40	16.00
getBioProbes	0.91	0.05	0.95
getOutliers	43.95	1.08	45.49
getQCRatios	9.58	0.30	9.87
getRatioProbes	1.25	0.04	1.30
getSpikeProbes	1.17	0.05	1.22
probeSelectionInterface	0	0	0
reprodPlot	0	0	0
yaqc.affy	9.43	0.30	9.72
yaqc.plot	10.00	0.15	10.16
yaqc.summary	9.70	0.14	9.84