Package: tilingArray

Version: 1.10.0

Command: D:\biocbld\1.8d\R\bin\R.exe CMD check tilingArray_1.10.0.tar.gz

RetCode: 1

Time: 84.5 seconds

Status: ERROR

CheckDir: tilingArray.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory 'D:/biocbld/1.8d/Rpacks/tilingArray.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'tilingArray/DESCRIPTION' ... OK
* this is package 'tilingArray' version '1.10.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'tilingArray' 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 library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* creating tilingArray-Ex.R ... OK
* checking examples ... ERROR
Running examples in tilingArray-Ex.R failed.
The error most likely occurred in:

> ### * class-segmentation
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: segmentation
> ### Title: The class segmentation represents a segmentation result.
> ### Aliases: segmentation-class confint logLik confint,segmentation-method
> ###   logLik,segmentation-method plot,segmentation-method
> ###   show,segmentation-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## generate random data with 5 segments:
> y = unlist(lapply(c(0,3,0.5,1.5,5), function(m) rnorm(10, mean=m)))
> 
> seg = segment(y, maxseg=10, maxk=15)
> seg = confint(seg, parm=c(3,4,5))
Error: could not find function "confint.breakpointsfull"
Execution halted

installing R.css in D:/biocbld/1.8d/Rpacks/tilingArray.Rcheck


---------- Making package tilingArray ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making findsegments.d from findsegments.c
making sampleStep.d from sampleStep.c
gcc   -Id:/biocbld/1.8d/R/include -Wall -O2   -c findsegments.c -o findsegments.o
gcc   -Id:/biocbld/1.8d/R/include -Wall -O2   -c sampleStep.c -o sampleStep.o
windres --include-dir d:/biocbld/1.8d/R/include  -i tilingArray_res.rc -o tilingArray_res.o
gcc  -shared -s  -o tilingArray.dll tilingArray.def findsegments.o sampleStep.o tilingArray_res.o  -Ld:/biocbld/1.8d/R/bin   -lR
  ... DLL made
  installing DLL
  installing R files
  save image
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: affy
Loading required package: affyio
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: strucchange
Loading required package: zoo
Loading required package: sandwich
Loading required package: colorspace

Attaching package: 'colorspace'


	The following object(s) are masked from package:grDevices :

	 hcl 

Loading required package: vsn
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: geneplotter
Loading required package: annotate
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
  installing inst files
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'tilingArray'
     Formats: text html latex example chm 
  breakpointsPretend                text    html    latex           chm
  class-segmentation                text    html    latex   example chm
  comparisonPlot                    text    html    latex   example chm
  costMatrix                        text    html    latex   example chm
  findsegments                      text    html    latex   example chm
  normalizeByReference              text    html    latex   example chm
  otherStrand                       text    html    latex   example chm
  plotAlongChrom                    text    html    latex   example chm
  posMin                            text    html    latex   example chm
  readCel2eSet                      text    html    latex   example chm
  sampleStep                        text    html    latex   example chm
  segment                           text    html    latex   example chm
  tilingArray-package               text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\1.8d\Rpacks\tilingArray.Rcheck\00_pkg_src\tilingArray\chm\tilingArray.chm


Compile time: 0 minutes, 0 seconds
14	Topics
44	Local links
2	Internet links
1	Graphic


Created d:\biocbld\1.8d\Rpacks\tilingArray.Rcheck\00_pkg_src\tilingArray\chm\tilingArray.chm, 39,503 bytes
Compression decreased file by 17,505 bytes.
  adding MD5 sums

* DONE (tilingArray)