Package: beadarraySNP

Version: 1.1.8

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check beadarraySNP_1.1.8.tar.gz

RetCode: 0

Time: 155.1 seconds

Status: WARNINGS

CheckDir: beadarraySNP.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory '/Users/biocbuild/2.0d/Rpacks/beadarraySNP.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-10-21 r39702)
* checking for file 'beadarraySNP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'beadarraySNP' version '1.1.8'
* checking package dependencies ... WARNING
'library' or 'require' calls not declared from:
  affy
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 'beadarraySNP' 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:
  calculateGSR calculateLOH pdfChromosomeGainLossLOH renameOPA
  reportChromosomeGainLossLOH reportGenomeGainLossLOH
  smoothed.intensity
Undocumented S4 methods:
  generic 'calculateGSR' and siglist 'SnpSetIllumina'
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 beadarraySNP-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating beadarraySNP-manual.tex ... OK
* checking beadarraySNP-manual.tex ... OK

WARNING: There were 2 warnings, see
  /Users/biocbuild/2.0d/Rpacks/beadarraySNP.Rcheck/00check.log
for details

* Installing *source* package 'beadarraySNP' ...
** R
** data
** 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: limma
Loading required package: quantsmooth
Loading required package: quantreg
Loading required package: SparseM
Package SparseM (0.71) loaded.  To cite, see citation("SparseM")
Loading required package: lodplot
Loading required package: grid
** help
 >>> Building/Updating help pages for package 'beadarraySNP'
     Formats: text html latex example 
  Datasets                          text    html    latex
  GenomicReports                    text    html    latex   example
  PolarTransforms                   text    html    latex   example
  QCIllumina-class                  text    html    latex
  arrayType                         text    html    latex
  backgroundCorrect.SNP             text    html    latex   example
  backgroundEstimate                text    html    latex   example
  calculateQCarray                  text    html    latex   example
  class.SnpSetIllumina              text    html    latex
  compareGenotypes                  text    html    latex   example
  heterozygosity                    text    html    latex   example
  heterozygousSNPs                  text    html    latex   example
  normalizeBetweenAlleles.SNP       text    html    latex   example
  normalizeLoci.SNP                 text    html    latex   example
  normalizeWithinArrays.SNP         text    html    latex   example
  pdfChromosomesSmoothCopyNumber    text    html    latex   example
  pdfQC                             text    html    latex
  plotQC                            text    html    latex   example
  read.SnpSetIllumina               text    html    latex   example
  removeLowQualityProbes            text    html    latex
  removeLowQualitySamples           text    html    latex   example
  reportSamplePanelQC-methods       text    html    latex   example
  standardNormalization             text    html    latex   example
** building package indices ...
* DONE (beadarraySNP)