Package: BeadExplorer

Version: 1.0.0

Command: /loc/biocbuild/1.9d/R/bin/R CMD check BeadExplorer_1.0.0.tar.gz

RetCode: 0

Time: 182.8 seconds

Status: WARNINGS

CheckDir: BeadExplorer.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/1.9d/Rpacks/BeadExplorer.Rcheck'
* using R version 2.4.0 alpha (2006-09-10 r39242)
* checking for file 'BeadExplorer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BeadExplorer' version '1.0.0'
* checking package dependencies ... WARNING
package 'methods' is used but not declared
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 'BeadExplorer' 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 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 S4 methods:
  generic 'annotation<-' and siglist 'beadQC,ANY'
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 BeadExplorer-Ex.R ... OK
* checking examples ... OK
* creating BeadExplorer-manual.tex ... OK
* checking BeadExplorer-manual.tex ... OK

WARNING: There were 2 warnings, see
  /extra/loc/biocbuild/1.9d/Rpacks/BeadExplorer.Rcheck/00check.log
for details

* Installing *source* package 'BeadExplorer' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: widgetTools

Loading Tcl/Tk interface ... done
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: R2HTML

Loading required package: tkWidgets

Loading required package: DynDoc

** help
 >>> Building/Updating help pages for package 'BeadExplorer'
     Formats: text html latex example 
  addManifest                       text    html    latex   example
  batchAnalysis                     text    html    latex   example
  beadAnalysis                      text    html    latex   example
  beadData-accessor                 text    html    latex
  beadData-class                    text    html    latex   example
  beadQC-class                      text    html    latex   example
  boxplotArrays                     text    html    latex   example
  boxplotQC                         text    html    latex   example
  clusterplot                       text    html    latex   example
  cutoff                            text    html    latex   example
  detectionCalls                    text    html    latex   example
  dotplotArrays                     text    html    latex   example
  dotplotQC                         text    html    latex   example
  examplebeadData                   text    html    latex   example
  examplebeadQC                     text    html    latex   example
  extract                           text    html    latex   example
  filterData                        text    html    latex   example
  getAnnot                          text    html    latex   example
  getArrayStats                     text    html    latex   example
  getDet                            text    html    latex   example
  getExprs                          text    html    latex   example
  getID                             text    html    latex   example
  getQC                             text    html    latex   example
  htmloutput                        text    html    latex   example
  multiDensity                      text    html    latex   example
  multiecdf                         text    html    latex   example
  normalise                         text    html    latex   example
  pc                                text    html    latex   example
  plotSamples                       text    html    latex   example
  readBead                          text    html    latex   example
  readManifest                      text    html    latex   example
  readQC                            text    html    latex   example
  scatterPlot                       text    html    latex   example
  write.beadData                    text    html    latex   example
  writeQC                           text    html    latex   example
** building package indices ...
* DONE (BeadExplorer)