Package: Category

Version: 2.1.8

Command: /loc/biocbuild/2.0d/R/bin/R CMD check Category_2.1.8.tar.gz

RetCode: 0

Time: 118.5 seconds

Status: WARNINGS

CheckDir: Category.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/loc/biocbuild/2.0d/Rpacks/Category.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'Category/DESCRIPTION' ... OK
* this is package 'Category' version '2.1.8'
* 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 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 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 ... WARNING
Undocumented code objects:
  GO2AllProbes ID2EntrezID ID2GO
Undocumented S4 classes:
  AffyDatPkg AffyDBPkg DatPkg DBPkg OrganismMappingDatPkg
  OrganismMappingDBPkg YeastDatPkg YeastDBPkg
Undocumented S4 methods:
  generic 'GO2AllProbes' and siglist 'DatPkg'
  generic 'GO2AllProbes' and siglist 'OrganismMappingDatPkg'
  generic 'ID2EntrezID' and siglist 'AffyDatPkg'
  generic 'ID2EntrezID' and siglist 'YeastDatPkg'
  generic 'ID2EntrezID' and siglist 'OrganismMappingDatPkg'
  generic 'ID2GO' and siglist 'DatPkg'
  generic 'ID2GO' and siglist 'OrganismMappingDatPkg'
  generic 'initialize' and siglist 'HyperGParams'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating Category-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating Category-manual.tex ... OK
* checking Category-manual.tex ... OK

WARNING: There was 1 warning, see
  /loc/biocbuild/2.0d/Rpacks/Category.Rcheck/00check.log
for details

* 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: GO
Loading required package: graph
Loading required package: annotate
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Creating a new generic function for "summary" in "Category"
** help
 >>> Building/Updating help pages for package 'Category'
     Formats: text html latex example 
  GOHyperGParams-class              text    html    latex
  HyperGParams-class                text    html    latex
  HyperGResult-class                text    html    latex
  HyperGResultBase-class            text    html    latex
  KEGGHyperGParams-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
  geneGoHyperGeoTest                text    html    latex
  geneKeggHyperGeoTest              text    html    latex
  getPathNames                      text    html    latex   example
  hyperGTest                        text    html    latex
  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)