Package: affycomp

Version: 1.14.0

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check affycomp_1.14.0.tar.gz

RetCode: 0

Time: 221.1 seconds

Status: OK

CheckDir: affycomp.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/affycomp.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'affycomp/DESCRIPTION' ... OK
* this is package 'affycomp' version '1.14.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affycomp' 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 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
affycomp: no visible binding for global variable 'mas5.assessment'
read.dilution: no visible binding for global variable
  'dilution.phenodata'
read.spikein: no visible binding for global variable
  'spikein.phenodata'
read.spikein: no visible binding for global variable
  'hgu133a.spikein.phenodata'
remove.hgu133a.xhyb: no visible binding for global variable
  'hgu133a.spikein.xhyb'
* 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
* checking data for non-ASCII characters ... OK
* creating affycomp-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating affycomp-manual.tex ... OK
* checking affycomp-manual.tex ... OK

* Installing *source* package 'affycomp' ...
** R
** data
** inst
** preparing package 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)'.

** help
 >>> Building/Updating help pages for package 'affycomp'
     Formats: text html latex example 
  SD                                text    html    latex   example
  affycomp.compfigs.auxiliary       text    html    latex   example
  affycomp.figures.auxiliary        text    html    latex   example
  affycomp.table                    text    html    latex   example
  affycompPlot                      text    html    latex   example
  assessAll                         text    html    latex
  assessDilution                    text    html    latex
  assessSD                          text    html    latex
  assessSpikeIn                     text    html    latex
  assessSpikeIn2                    text    html    latex
  dilution.phenodata                text    html    latex
  exprset.log                       text    html    latex
  hgu133a.spikein.phenodata         text    html    latex
  lw.sd.assessment                  text    html    latex
  mas5.assessment                   text    html    latex
  readin                            text    html    latex
  remove.hgu133a.xhyb               text    html    latex
  rma.assessment                    text    html    latex
  rma.sd.assessment                 text    html    latex
  spikein.phenodata                 text    html    latex
  xhyb                              text    html    latex
** building package indices ...
* DONE (affycomp)