Package: quantsmooth

Version: 1.1.2

Command: E:\biocbld\2.0d\R\bin\R.exe CMD check quantsmooth_1.1.2.tar.gz

RetCode: 1

Time: 421.3 seconds

Status: ERROR

CheckDir: quantsmooth.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory 'E:/biocbld/2.0d/Rpacks/quantsmooth.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'quantsmooth/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'quantsmooth' version '1.1.2'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'quantsmooth' 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 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 ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'getChangedRegions':
getChangedRegions
  Code: function(intensities, positions, normalized.to = 1, interval,
                 threshold, minlength = 2, ...)
  Docs: function(intensities, positions, normalized.to = 1,
                 smooth.lambda = 2, interval, threshold, minlength = 2)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    smooth.lambda
  Mismatches in argument names (first 3):
    Position: 4 Code: interval Docs: smooth.lambda
    Position: 5 Code: threshold Docs: interval
    Position: 6 Code: minlength Docs: threshold

* checking Rd \usage sections ... OK
* creating quantsmooth-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating quantsmooth-manual.tex ... OK
* checking quantsmooth-manual.tex ... ERROR
LaTeX errors when creating DVI version.
This typically indicates Rd problems.

installing R.css in E:/biocbld/2.0d/Rpacks/quantsmooth.Rcheck


---------- Making package quantsmooth ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'quantsmooth'
     Formats: text html latex example chm 
  Chromosome14                      text    html    latex           chm
  drawSimpleChrom                   text    html    latex   example chm
  getChangedIdx                     text    html    latex           chm
  getChangedRegions                 text    html    latex   example chm
  getLambdaMin                      text    html    latex   example chm
  lengthChromosome                  text    html    latex   example chm
  numericCHR                        text    html    latex   example chm
  paintCytobands                    text    html    latex   example chm
  plotChromosome                    text    html    latex           chm
  plotSmoothed                      text    html    latex   example chm
  prepareGenomePlot                 text    html    latex           chm
  quantsmooth                       text    html    latex   example chm
  quantsmooth.cv                    text    html    latex   example chm
  scaleto                           text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\2.0d\Rpacks\quantsmooth.Rcheck\00_pkg_src\quantsmooth\chm\quantsmooth.chm


Compile time: 0 minutes, 0 seconds
15	Topics
45	Local links
0	Internet links
1	Graphic


Created e:\biocbld\2.0d\Rpacks\quantsmooth.Rcheck\00_pkg_src\quantsmooth\chm\quantsmooth.chm, 29,722 bytes
Compression decreased file by 12,801 bytes.
  adding MD5 sums

* DONE (quantsmooth)