Package: MCRestimate

Version: 1.10.0

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check MCRestimate_1.10.0.tar.gz

RetCode: 0

Time: 351.1 seconds

Status: OK

CheckDir: MCRestimate.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/MCRestimate.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'MCRestimate/DESCRIPTION' ... OK
* this is package 'MCRestimate' version '1.10.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'MCRestimate' can be installed ... 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 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
Found possibly global 'T' or 'F' in the following function:
  SVM.OVA.wrap
* 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 ... NOTE
S3 methods shown with full name in documentation object 'PLR':
  predict.PLR

S3 methods shown with full name in documentation object 'plot.MCRestimate':
  plot.MCRestimate

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* creating MCRestimate-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating MCRestimate-manual.tex ... OK
* checking MCRestimate-manual.tex ... OK

* Installing *source* package 'MCRestimate' ...
** R
** inst
** preparing package for lazy loading
Loading required package: e1071
Loading required package: class
Loading required package: pamr
Loading required package: cluster
Loading required package: survival
Loading required package: splines
Loading required package: randomForest
randomForest 4.5-18 
Type rfNews() to see new features/changes/bug fixes.
Loading required package: RColorBrewer
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: golubEsets
Loading required package: arrayMagic
Loading required package: vsn
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: limma
Loading required package: genefilter
Loading required package: gpls
Loading required package: ROC

Attaching package: 'ROC'


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

	 AUC,
	 pAUC 

** help
 >>> Building/Updating help pages for package 'MCRestimate'
     Formats: text html latex example 
  ClassifierBuild                   text    html    latex   example
  MCRconfusion                      text    html    latex   example
  MCRestimate                       text    html    latex   example
  MCRestimateMerge                  text    html    latex   example
  PLR                               text    html    latex   example
  PLR.add.fkt                       text    html    latex   example
  SVM.OVA.wrap                      text    html    latex   example
  class.factor.format               text    html    latex   example
  gene.reduction.fkt                text    html    latex   example
  geneReduction                     text    html    latex   example
  important.variable.names          text    html    latex   example
  intersectList                     text    html    latex   example
  plot.MCRestimate                  text    html    latex   example
  replace.NA                        text    html    latex   example
  select.NA.elements                text    html    latex   example
  whatiscorrect                     text    html    latex   example
  wrapper.fkt                       text    html    latex   example
** building package indices ...
* DONE (MCRestimate)