Package: cghMCR

Version: 1.7.2

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check cghMCR_1.7.2.tar.gz

RetCode: 0

Time: 55.5 seconds

Status: WARNINGS

CheckDir: cghMCR.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/cghMCR.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'cghMCR/DESCRIPTION' ... OK
* this is package 'cghMCR' version '1.7.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'cghMCR' 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 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 Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'cghMCR':
cghMCR
  Code: function(segments, gapAllowed = 500, alteredLow = 0.03,
                 alteredHigh = 0.97, spanLimit = 2e+07, recurrence =
                 75, thresholdType = c("quantile", "value"))
  Docs: function(segments, gapAllowed = 500, alteredLow = 0.03,
                 alteredHigh = 0.97, spanLimit = 2e+07, recurrence =
                 75)
  Argument names in code not in docs:
    thresholdType

* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating cghMCR-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating cghMCR-manual.tex ... OK
* checking cghMCR-manual.tex ... OK

WARNING: There was 1 warning, see
  /home/biocbuild/bbs-2.1-bioc/meat/cghMCR.Rcheck/00check.log
for details

* Installing *source* package 'cghMCR' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: DNAcopy
Loading required package: marray
Loading required package: limma
Loading required package: arrayQuality
Loading required package: convert
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: hexbin
Loading required package: grid
Loading required package: lattice
Loading required package: gridBase
Loading required package: RColorBrewer
Warning in namespaceImportFrom(self, asNamespace(ns)) :
  replacing previous import: summary
Creating a new generic function for "print" in "cghMCR"
** help
 >>> Building/Updating help pages for package 'cghMCR'
     Formats: text html latex example 
  cghMCR-class                      text    html    latex   example
  cghMCR                            text    html    latex   example
  mergeMCRProbes                    text    html    latex   example
  plot.DNAcopy                      text    html    latex   example
** building package indices ...
* DONE (cghMCR)