Package: oligoClasses

Version: 0.0.2

Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check oligoClasses_0.0.2.tar.gz

RetCode: 0

Time: 34.7 seconds

Status: WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.1-bioc/meat/oligoClasses.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '0.0.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'oligoClasses' 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 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 whether the name space 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 ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  calls calls<- callsConfidence callsConfidence<- cnConfidence
  cnConfidence<- copyNumber copyNumber<-
Undocumented S4 classes:
  AffySNPCNVPDInfo DBPDInfo ExonFeatureSet ExpressionFeatureSet
  FeatureSet oligoSnpSet PDInfo platformDesign QuantificationSet
  SnpCallSet SnpCnvFeatureSet SNPCNVPDInfo SnpCnvQSet SnpCopyNumberSet
  SnpFeatureSet SNPPDInfo SnpQSet TilingFeatureSet
Undocumented S4 methods:
  generic 'calls' and siglist 'SnpCallSet'
  generic 'calls' and siglist 'oligoSnpSet'
  generic 'calls<-' and siglist 'SnpCallSet,matrix'
  generic 'calls<-' and siglist 'oligoSnpSet,matrix'
  generic 'callsConfidence' and siglist 'SnpCallSet'
  generic 'callsConfidence' and siglist 'oligoSnpSet'
  generic 'callsConfidence<-' and siglist 'SnpCallSet,matrix'
  generic 'callsConfidence<-' and siglist 'oligoSnpSet,matrix'
  generic 'cnConfidence' and siglist 'SnpCopyNumberSet'
  generic 'cnConfidence' and siglist 'oligoSnpSet'
  generic 'cnConfidence<-' and siglist 'SnpCopyNumberSet,matrix'
  generic 'cnConfidence<-' and siglist 'oligoSnpSet,matrix'
  generic 'copyNumber' and siglist 'SnpCopyNumberSet'
  generic 'copyNumber' and siglist 'oligoSnpSet'
  generic 'copyNumber<-' and siglist 'SnpCopyNumberSet,matrix'
  generic 'copyNumber<-' and siglist 'oligoSnpSet,matrix'
  generic 'initialize' and siglist 'SnpCallSet'
  generic 'initialize' and siglist 'SnpCopyNumberSet'
  generic 'initialize' and siglist 'oligoSnpSet'
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 DVI version of manual ... OK

WARNING: There was 1 warning, see
  E:/biocbld/bbs-2.1-bioc/meat/oligoClasses.Rcheck/00check.log
for details

installing R.css in E:/biocbld/bbs-2.1-bioc/meat/oligoClasses.Rcheck


---------- Making package oligoClasses ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  preparing package oligoClasses for lazy loading
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)'.

  no man files in this package
  installing indices
  installing help
  adding MD5 sums

* DONE (oligoClasses)