Package: altcdfenvs

Version: 1.11.0

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check altcdfenvs_1.11.0.tar.gz

RetCode: 0

Time: 225.1 seconds

Status: OK

CheckDir: altcdfenvs.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/altcdfenvs.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'altcdfenvs/DESCRIPTION' ... OK
* this is package 'altcdfenvs' version '1.11.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'altcdfenvs' 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 ... OK
* 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 'plot.CdfEnvAffy':
  plot.CdfEnvAffy

S3 methods shown with full name in documentation object 'unique.CdfEnvAffy':
  unique.CdfEnvAffy

S3 methods shown with full name in documentation object 'read.FASTA.entry':
  print.FASTA

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'.
* checking data for non-ASCII characters ... OK
* creating altcdfenvs-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating altcdfenvs-manual.tex ... OK
* checking altcdfenvs-manual.tex ... OK

* Installing *source* package 'altcdfenvs' ...
** 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)'.

Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: matchprobes
Loading required package: makecdfenv
Creating a new generic function for "plot" in "altcdfenvs"
** help
Note: unmatched right brace in 'cdfenvEx' on or after line 21
 >>> Building/Updating help pages for package 'altcdfenvs'
     Formats: text html latex example 
  CdfEnvAffy-class                  text    html    latex   example
  appendCdfEnvAffy                  text    html    latex   example
  cdfenv                            text    html    latex   example
  cdfenvEx                          text    html    latex   example
  copyCdfEnvAffy                    text    html    latex
  countduplicated                   text    html    latex   example
  geneNames                         text    html    latex
  getxy.probeseq                    text    html    latex   example
  index2xy                          text    html    latex   example
  indexProbes.CdfEnvAffy            text    html    latex   example
  plot.CdfEnvAffy                   text    html    latex   example
  removeIndex                       text    html    latex   example
  unique.CdfEnvAffy                 text    html    latex   example
  utils.FASTA                       text    html    latex   example
  validAffyBatch                    text    html    latex   example
** building package indices ...
* DONE (altcdfenvs)