Package: GOstats

Version: 2.0.0

Command: D:\biocbld\1.9d\R\bin\R.exe CMD check GOstats_2.0.0.tar.gz

RetCode: 0

Time: 328.6 seconds

Status: WARNINGS

CheckDir: GOstats.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory 'D:/biocbld/1.9d/Rpacks/GOstats.Rcheck'
* using R version 2.4.0 (2006-10-03)
* checking for file 'GOstats/DESCRIPTION' ... OK
* this is package 'GOstats' version '2.0.0'
* checking package dependencies ... OK
* 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 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 ... OK
* 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' ... OK
* creating GOstats-manual.tex ... OK
* checking GOstats-manual.tex ... OK

WARNING: There was 1 warning, see
  D:/biocbld/1.9d/Rpacks/GOstats.Rcheck/00check.log
for details

installing R.css in D:/biocbld/1.9d/Rpacks/GOstats.Rcheck


---------- Making package GOstats ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'GOstats'
     Formats: text html latex example chm 
  GOHyperG                          text    html    latex   example chm
  GOHyperGResult-class              text    html    latex           chm
  GOLeaves                          text    html    latex   example chm
  GOstats-defunct                   text    html    latex           chm
  GOstats-package                   text    html    latex           chm
  Ndists                            text    html    latex   example chm
  compCorrGraph                     text    html    latex   example chm
  compGdist                         text    html    latex   example chm
  hyperG2Affy                       text    html    latex   example chm
  hyperGTest                        text    html    latex           chm
  hyperGtable                       text    html    latex   example chm
  idx2dimnames                      text    html    latex   example chm
  makeGOGraph                       text    html    latex   example chm
  notConn                           text    html    latex   example chm
  oneGOGraph                        text    html    latex   example chm
  probeSetSummary                   text    html    latex           chm
  shortestPath                      text    html    latex   example chm
  simLL                             text    html    latex   example chm
  triadCensus                       text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\1.9d\Rpacks\GOstats.Rcheck\00_pkg_src\GOstats\chm\GOstats.chm


Compile time: 0 minutes, 0 seconds
20	Topics
78	Local links
0	Internet links
1	Graphic


Created d:\biocbld\1.9d\Rpacks\GOstats.Rcheck\00_pkg_src\GOstats\chm\GOstats.chm, 47,372 bytes
Compression decreased file by 36,024 bytes.
  preparing package GOstats for lazy loading
Loading required package: graph
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: GO
Loading required package: annotate
Loading required package: RBGL
Loading required package: Category
Loading required package: KEGG
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
  adding MD5 sums

* DONE (GOstats)