Package: made4

Version: 1.12.1

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check made4_1.12.1.tar.gz

RetCode: 0

Time: 161.0 seconds

Status: OK

CheckDir: made4.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/made4.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'made4/DESCRIPTION' ... OK
* this is package 'made4' version '1.12.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'made4' 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
getdata: no visible binding for global variable 'intensities'
* 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 'bga':
  plot.bga

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

S3 methods shown with full name in documentation object 'comparelists':
  print.comparelists

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

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

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 made4-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating made4-manual.tex ... OK
* checking made4-manual.tex ... OK

* Installing *source* package 'made4' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: ade4

Attaching package: 'ade4'


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

	 within 

** help
Note: unmatched right brace in 'cia' on or after line 102
Note: unmatched right brace in 'genes' on or after line 40
Note: unmatched right brace in 'jmol3D' on or after line 42
Note: unmatched right brace in 'plotgenes' on or after line 48
 >>> Building/Updating help pages for package 'made4'
     Formats: text html latex example 
  NCI60                             text    html    latex   example
  array2ade4                        text    html    latex   example
  bet.coinertia                     text    html    latex   example
  between.graph                     text    html    latex   example
  bga                               text    html    latex   example
  bga.jackknife                     text    html    latex   example
  bga.suppl                         text    html    latex   example
  checkfac                          text    html    latex   example
  chime3D                           text    html    latex   example
  cia                               text    html    latex   example
  commonMap                         text    html    latex   example
  comparelists                      text    html    latex   example
  do3d                              text    html    latex   example
  dudi.rwcoa                        text    html    latex   example
  forrwcoa                          text    html    latex   example
  genes                             text    html    latex   example
  genes1d                           text    html    latex   example
  getcol                            text    html    latex   example
  getdata                           text    html    latex   example
  graph1D                           text    html    latex   example
  heatplot                          text    html    latex   example
  html3D                            text    html    latex   example
  jmol3D                            text    html    latex   example
  khan                              text    html    latex   example
  ord                               text    html    latex   example
  overview                          text    html    latex   example
  plotarrays                        text    html    latex   example
  plotgenes                         text    html    latex   example
  pretty.dend                       text    html    latex   example
  randomiser                        text    html    latex   example
  s.var                             text    html    latex   example
  sumstats                          text    html    latex   example
  suppl                             text    html    latex   example
  topgenes                          text    html    latex   example
** building package indices ...
* DONE (made4)