Package: affycoretools

Version: 1.5.9

Command: /home/biocbuild/1.9d/R/bin/R CMD check affycoretools_1.5.9.tar.gz

RetCode: 0

Time: 95.6 seconds

Status: WARNINGS

CheckDir: affycoretools.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/home/biocbuild/1.9d/Rpacks/affycoretools.Rcheck'
* using R version 2.4.0 alpha (2006-09-10 r39242)
* checking for file 'affycoretools/DESCRIPTION' ... OK
* this is package 'affycoretools' version '1.5.9'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affycoretools' 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 syntax errors ... OK
* checking R files for non-ASCII characters ... 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 ... WARNING
Loading required package: methods

Error in if (mustFind) stop(gettextf("no generic function found for '%s'",  : 
	argument is not interpretable as logical
In addition: Warning message:
the condition has length > 1 and only the first element will be used in: if (mustFind) stop(gettextf("no generic function found for '%s'",  
Execution halted

A namespace must be able to be loaded with just the base namespace loaded:
otherwise if the namespace gets loaded by a saved object, the session will
be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 ... OK
* creating affycoretools-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating affycoretools-manual.tex ... OK
* checking affycoretools-manual.tex ... OK

WARNING: There was 1 warning, see
  /home/biocbuild/1.9d/Rpacks/affycoretools.Rcheck/00check.log
for details

* Installing *source* package 'affycoretools' ...
** R
** inst
** preparing package for lazy loading
Loading required package: affy

Loading required package: Biobase

Loading required package: tools


Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: affyio

Loading required package: limma

Loading required package: GOstats

Loading required package: graph

Loading required package: Ruuid

Loading required package: GO

Loading required package: annotate

Loading required package: RBGL

Loading required package: genefilter

Loading required package: survival

Loading required package: splines

Loading required package: multtest

Loading required package: Category

Loading required package: KEGG

Loading required package: hgu95av2

Loading required package: biomaRt

Loading required package: XML


Attaching package: 'XML'


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

	 addNode 

Loading required package: RCurl


Attaching package: 'biomaRt'


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

	 getGO 

** help
 >>> Building/Updating help pages for package 'affycoretools'
     Formats: text html latex example 
  affystart                         text    html    latex
  annBM                             text    html    latex   example
  convert.back                      text    html    latex
  foldFilt                          text    html    latex
  foldFiltBM                        text    html    latex
  getCols                           text    html    latex
  getIndex                          text    html    latex
  getSymbol                         text    html    latex
  getans                            text    html    latex
  hyperG2annaffy                    text    html    latex
  intNames                          text    html    latex
  limma2annaffy                     text    html    latex
  limma2biomaRt                     text    html    latex
  make.cl                           text    html    latex
  makeIndices                       text    html    latex
  pca.legend                        text    html    latex
  plotDeg                           text    html    latex   example
  plotMA                            text    html    latex
  plotPCA                           text    html    latex
  probes2table                      text    html    latex
  probes2tableBM                    text    html    latex
  tableFilt                         text    html    latex
  vennCounts2                       text    html    latex   example
  vennSelect                        text    html    latex
  vennSelectBM                      text    html    latex
** building package indices ...
* DONE (affycoretools)