Package: arrayQualityMetrics

Version: 1.8.1

Command: E:\biocbld\bbs-2.3-bioc\R\bin\R.exe CMD check --no-vignettes arrayQualityMetrics_1.8.1.tar.gz

StartedAt: 2009-04-18 18:08:42 -0700 (Sat, 18 Apr 2009)

EndedAt: 2009-04-18 18:10:18 -0700 (Sat, 18 Apr 2009)

EllapsedTime: 96.2 seconds

RetCode: 0

Status: OK

CheckDir: arrayQualityMetrics.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/arrayQualityMetrics.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'arrayQualityMetrics/DESCRIPTION' ... OK
* this is package 'arrayQualityMetrics' version '1.8.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'arrayQualityMetrics' 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 name space can be loaded with stated dependencies ... 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 ... NOTE
arrayQualityMetrics,BeadLevelList: no visible binding for global
  variable 'sec3text'
arrayQualityMetrics,BeadLevelList: no visible binding for global
  variable 'gctext'
arrayQualityMetrics,BeadLevelList: no visible binding for global
  variable 'legendgc'
arrayQualityMetrics,BeadLevelList: no visible binding for global
  variable 'gotext'
arrayQualityMetrics,BeadLevelList: no visible binding for global
  variable 'legendgo'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating arrayQualityMetrics-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating arrayQualityMetrics-manual.tex ... OK
* checking arrayQualityMetrics-manual.tex using pdflatex ... OK

installing R.css in E:/biocbld/bbs-2.3-bioc/meat/arrayQualityMetrics.Rcheck


---------- Making package arrayQualityMetrics ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  preparing package arrayQualityMetrics for lazy loading
Loading required package: Biobase
Loading required package: tools

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: geneplotter
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: xtable
KernSmooth 2.22 installed
Copyright M. P. Wand 1997

Attaching package: 'geneplotter'


	The following object(s) are masked from package:lattice :

	 panel.smoothScatter 

Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: vsn
Loading required package: affy
Loading required package: limma
Loading required package: RColorBrewer
Loading required package: affyPLM
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: preprocessCore
Loading required package: simpleaffy
Loading required package: latticeExtra
Loading required package: grid
Loading required package: beadarray
Loading required package: hwriter
Loading required package: sma

Attaching package: 'beadarray'


	The following object(s) are masked from package:limma :

	 backgroundCorrect,
	 imageplot,
	 plotMA 

Loading required package: marray

Attaching package: 'marray'


	The following object(s) are masked from package:sma :

	 cor.na,
	 length.na,
	 log.na,
	 mean.na,
	 order.na,
	 prod.na,
	 quantile.na,
	 scale.na,
	 stat.gnames,
	 sum.na,
	 var.na 

  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'arrayQualityMetrics'
     Formats: text html latex example chm 
  XYfromGAL                         text    html    latex           chm
  arrayQualityMetrics               text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.3-bioc\meat\arrayQualityMetrics.Rcheck\00_pkg_src\arrayQualityMetrics\chm\arrayQualityMetrics.chm


Compile time: 0 minutes, 0 seconds
3	Topics
14	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.3-bioc\meat\arrayQualityMetrics.Rcheck\00_pkg_src\arrayQualityMetrics\chm\arrayQualityMetrics.chm, 19,652 bytes
Compression increased file by 583 bytes.
  adding MD5 sums

* DONE (arrayQualityMetrics)