Package: tilingArray

Version: 1.10.0

Command: /loc/biocbuild/1.8d/R/bin/R CMD check tilingArray_1.10.0.tar.gz

RetCode: 1

Time: 147.4 seconds

Status: ERROR

CheckDir: tilingArray.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/loc/biocbuild/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 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 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 *source* package 'tilingArray' ...
** libs
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -c findsegments.c -o findsegments.o
findsegments.c: In function 'findsegments_dp':
findsegments.c:104: warning: implicit declaration of function 'finite'
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -c sampleStep.c -o sampleStep.o
gcc -G -L/usr/local/lib -o tilingArray.so findsegments.o sampleStep.o   
** R
** inst
** 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
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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
** help
 >>> Building/Updating help pages for package 'tilingArray'
     Formats: text html latex example 
  breakpointsPretend                text    html    latex
  class-segmentation                text    html    latex   example
  comparisonPlot                    text    html    latex   example
  costMatrix                        text    html    latex   example
  findsegments                      text    html    latex   example
  normalizeByReference              text    html    latex   example
  otherStrand                       text    html    latex   example
  plotAlongChrom                    text    html    latex   example
  posMin                            text    html    latex   example
  readCel2eSet                      text    html    latex   example
  sampleStep                        text    html    latex   example
  segment                           text    html    latex   example
  tilingArray-package               text    html    latex
** building package indices ...
* DONE (tilingArray)