Package: GOstats

Version: 2.1.7

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check GOstats_2.1.7.tar.gz

RetCode: 0

Time: 308.8 seconds

Status: WARNINGS

CheckDir: GOstats.Rcheck

Warnings: 4

* checking for working latex ... OK
* using log directory '/Users/biocbuild/2.0d/Rpacks/GOstats.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-10-21 r39702)
* checking for file 'GOstats/DESCRIPTION' ... OK
* this is package 'GOstats' version '2.1.7'
* checking package dependencies ... WARNING
'library' or 'require' calls not declared from:
  SparseM
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking if this is a source package ... OK
* checking whether package 'GOstats' 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:
  plotTermGraphs selectedGenes sigCategories
All user-level objects in a package 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 GOstats-Ex.R ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: 'GOHyperG' is deprecated.
  Warning: 'hyperG2Affy' is deprecated.
  Warning: 'GOHyperG' is deprecated.
  Warning: 'hyperGtable' is deprecated.
  Warning: 'GOHyperG' is deprecated.
Deprecated functions may be defunct as soon as of the next release of R.
See ?Deprecated.
* checking package vignettes in 'inst/doc' ... WARNING
Package vignettes without corresponding PDF:
  /Users/biocbuild/2.0d/Rpacks/GOstats.Rcheck/00_pkg_src/GOstats/inst/doc/GOvis.Rnw
* creating GOstats-manual.tex ... OK
* checking GOstats-manual.tex ... OK

WARNING: There were 4 warnings, see
  /Users/biocbuild/2.0d/Rpacks/GOstats.Rcheck/00check.log
for details

* Installing *source* package 'GOstats' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: graph
Loading required package: GO
Loading required package: annotate
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: RBGL
Loading required package: Category
Loading required package: KEGG
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
** help
 >>> Building/Updating help pages for package 'GOstats'
     Formats: text html latex example 
  GOHyperG                          text    html    latex   example
  GOHyperGResult-class              text    html    latex
  GOLeaves                          text    html    latex   example
  GOstats-defunct                   text    html    latex
  GOstats-package                   text    html    latex
  Ndists                            text    html    latex   example
  compCorrGraph                     text    html    latex   example
  compGdist                         text    html    latex   example
  hyperG2Affy                       text    html    latex   example
  hyperGTest                        text    html    latex
  hyperGtable                       text    html    latex   example
  idx2dimnames                      text    html    latex   example
  makeGOGraph                       text    html    latex   example
  notConn                           text    html    latex   example
  oneGOGraph                        text    html    latex   example
  probeSetSummary                   text    html    latex
  shortestPath                      text    html    latex   example
  simLL                             text    html    latex   example
  triadCensus                       text    html    latex   example
** building package indices ...
* DONE (GOstats)