Package: yaqcaffy

Version: 1.10.1

Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings yaqcaffy_1.10.1.tar.gz

StartedAt: 2011-03-31 11:22:01 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 11:26:12 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 251.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: yaqcaffy.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/yaqcaffy.Rcheck'
* using R version 2.12.2 (2011-02-25)
* 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 '1.10.1'
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'plot' when loading 'graphics'
  Warning: replacing previous import 'plot' when loading 'graphics'
See 'D:/biocbld/bbs-2.7-bioc/meat/yaqcaffy.Rcheck/00install.out' for details.
* 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 ... OK
* 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-2.7-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
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: genefilter
Loading required package: gcrma
Warning: replacing previous import 'plot' when loading 'graphics'
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
Warning: replacing previous import 'plot' when loading 'graphics'

* DONE (yaqcaffy)

name	user	system	elapsed
YaqcControlProbes-class	0.02	0.00	0.02
getAllInt	15.82	0.35	16.20
getBioProbes	0.91	0.03	0.94
getOutliers	45.28	0.95	46.46
getQCRatios	9.14	0.22	9.36
getRatioProbes	1.10	0.08	1.18
getSpikeProbes	1.17	0.02	1.18
probeSelectionInterface	0	0	0
reprodPlot	0	0	0
yaqc.affy	8.83	0.09	8.92
yaqc.plot	9.61	0.08	9.68
yaqc.summary	9.06	0.18	9.25