Package: Category

Version: 1.5.9

Command: /loc/biocbuild/1.9d/R/bin/R CMD check Category_1.5.9.tar.gz

RetCode: 1

Time: 220.9 seconds

Status: ERROR

CheckDir: Category.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/Category.Rcheck'
* using R version 2.4.0 Under development (unstable) (2006-07-18 r38641)
* checking for file 'Category/DESCRIPTION' ... OK
* this is package 'Category' version '1.5.9'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Category' 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 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 ... WARNING
Functions/methods with usage in documentation object 'GOHyperG' but not in code:
  GOHyperG

* checking Rd \usage sections ... OK
* creating Category-Ex.R ... OK
* checking examples ... ERROR
Running examples in Category-Ex.R failed.
The error most likely occurred in:

> ### * GOHyperG
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: GOHyperG
> ### Title: Hypergeometric Tests for GO
> ### Aliases: GOHyperG
> ### Keywords: htest
> 
> ### ** Examples
> 
> 
> library(hgu95av2)
> library(GO)
> w1<-as.list(hgu95av2LOCUSID)
Warning: 'hgu95av2LOCUSID' is deprecated.
Use 'hgu95av2ENTREZID' instead.
See help("Deprecated")
> w2<-unique(unlist(w1))
> set.seed(123)
> #pick a hundred interesting genes
>  myLL <- sample(w2, 100)
>  xx<-GOHyperG(myLL, lib="hgu95av2", what="MF")
Error: could not find function "GOHyperG"
Execution halted

* Installing *source* package 'Category' ...
** R
** 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()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: KEGG
Loading required package: hgu95av2
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: GO
Loading required package: graph
Loading required package: Ruuid
Loading required package: annotate
** help
 >>> Building/Updating help pages for package 'Category'
     Formats: text html latex example 
  GOHyperG                          text    html    latex   example
  GeneCategoryHyperGeoTestParams-cl text    html    latex
  GeneCategoryHyperGeoTestResult-cl text    html    latex
  GeneCategoryHyperGeoTestResultBas text    html    latex
  GeneGoHyperGeoTestParams-class    text    html    latex
  GeneKeggHyperGeoTestParams-class  text    html    latex
  MAPAmat                           text    html    latex   example
  applyByCategory                   text    html    latex   example
  cateGOryMatrix                    text    html    latex   example
  categoryToEntrezBuilder           text    html    latex
  findAMstats                       text    html    latex   example
  geneCategoryHyperGeoTest          text    html    latex
  geneGoHyperGeoTest                text    html    latex   example
  geneKeggHyperGeoTest              text    html    latex   example
  getPathNames                      text    html    latex   example
  makeEBcontr                       text    html    latex   example
  probes2MAP                        text    html    latex   example
  probes2Path                       text    html    latex   example
  ttperm                            text    html    latex   example
  universeBuilder                   text    html    latex
** building package indices ...
* DONE (Category)