Package: BeadExplorer

Version: 1.4.0

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check BeadExplorer_1.4.0.tar.gz

RetCode: 0

Time: 69.6 seconds

Status: OK

CheckDir: BeadExplorer.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/BeadExplorer.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'BeadExplorer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BeadExplorer' version '1.4.0'
* checking package dependencies ... OK
* 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 non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
batchAnalysis: no visible binding for global variable 'output'
beadAnalysis: no visible binding for global variable 'examplebeadData'
beadAnalysis: no visible binding for global variable 'examplebeadQC'
boxplotArrays: no visible binding for global variable 'oqc'
getQC2: no visible binding for global variable 'HumWG6'
getQC2: no visible binding for global variable 'HumRef8'
Found possibly global 'T' or 'F' in the following function:
  boxplotQC
* 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
* checking data for non-ASCII characters ... OK
* creating BeadExplorer-Ex.R ... OK
* checking examples ... OK
* creating BeadExplorer-manual.tex ... OK
* checking BeadExplorer-manual.tex ... OK

* Installing *source* package 'BeadExplorer' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: widgetTools
Loading required package: tcltk
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()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affyio
Loading required package: preprocessCore
Loading required package: R2HTML
Loading required package: tkWidgets
Loading required package: DynDoc
** help
Note: unmatched right brace in 'beadData-class' on or after line 61
Note: unmatched right brace in 'readQC' on or after line 23
Note: unmatched right brace in 'scatterPlot' on or after line 44
 >>> Building/Updating help pages for package 'BeadExplorer'
     Formats: text html latex example 
  HumRef8v1                         text    html    latex   example
  HumWG6v1                          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
  getQC2                            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)