Package: tilingArray

Version: 1.11.12

Command: /loc/biocbuild/1.9d/R/bin/R CMD check tilingArray_1.11.12.tar.gz

RetCode: 0

Time: 156.9 seconds

Status: WARNINGS

CheckDir: tilingArray.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/1.9d/Rpacks/tilingArray.Rcheck'
* using R version 2.4.0 alpha (2006-09-10 r39242)
* checking for file 'tilingArray/DESCRIPTION' ... OK
* this is package 'tilingArray' version '1.11.12'
* 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 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 ... WARNING
Creating a new generic function for 'plot' in 'colorspace'
Loading required package: methods

Error in paste(x[c("major", "minor")], collapse = ".") : 
	could not find function "getMethods"
Error: .onLoad failed in 'loadNamespace' for 'colorspace'
Error: unable to load R code in package 'tilingArray'
Execution halted

A namespace must be able to be loaded with just the base namespace loaded:
otherwise if the namespace gets loaded by a saved object, the session will
be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating tilingArray-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating tilingArray-manual.tex ... OK
* checking tilingArray-manual.tex ... OK

WARNING: There was 1 warning, see
  /extra/loc/biocbuild/1.9d/Rpacks/tilingArray.Rcheck/00check.log
for details

* Installing *source* package 'tilingArray' ...
** libs
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c findsegments.c -o findsegments.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c sampleStep.c -o sampleStep.o
gcc -shared -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


Attaching package: 'zoo'


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

	 rapply 

Loading required package: sandwich

Loading required package: colorspace

Creating a new generic function for 'plot' in '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
Loading required package: pixmap

** help
 >>> Building/Updating help pages for package 'tilingArray'
     Formats: text html latex example 
  PMindex                           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
  plotAlongChromLegend              text    html    latex   example
  plotFeatures                      text    html    latex   example
  plotSegmentationDots              text    html    latex   example
  plotSegmentationHeatmap           text    html    latex   example
  posMin                            text    html    latex   example
  qcPlots                           text    html    latex   example
  readCel2eSet                      text    html    latex   example
  sampleStep                        text    html    latex   example
  segChrom                          text    html    latex   example
  segment                           text    html    latex   example
  tilingArray-package               text    html    latex
** building package indices ...
* DONE (tilingArray)