BeadExplorer 1.5.0
Gareth Elvidge
| Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BeadExplorer | | Last Changed Rev: 27716 / Revision: 30951 | | Last Changed Date: 2007-10-02 18:16:39 -0700 (Tue, 02 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | ERROR | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | ERROR | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| pelham | Mac OS X Leopard (10.5.1) / i386 | OK | [ ERROR ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.2-bioc/meat/BeadExplorer.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ASCII
* checking for file 'BeadExplorer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BeadExplorer' version '1.5.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'BeadExplorer' 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 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 ... NOTE
batchAnalysis: no visible binding for global variable 'output'
beadAnalysis: no visible binding for global variable 'examplebeadData'
beadAnalysis: no visible binding for global variable 'examplebeadQC'
boxplotArrays: no visible binding for global variable 'oqc'
getQC2: no visible binding for global variable 'HumWG6'
getQC2: no visible binding for global variable 'HumRef8'
Found possibly global 'T' or 'F' in the following function:
boxplotQC
* 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 data for non-ASCII characters ... OK
* creating BeadExplorer-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'BeadExplorer-Ex.R' failed.
The error most likely occurred in:
> ### * beadData-class
>
> flush(stderr()); flush(stdout())
>
> ### Name: beadData-class
> ### Title: Class "beadData"
> ### Aliases: beadData-class [,beadData-method boxplot,beadData-method
> ### detectionCalls,beadData-method detExprs,beadData-method
> ### fileOrigin,beadData-method nGenes,beadData-method
> ### normMethod,beadData-method nSamples,beadData-method
> ### pairs,beadData-method param,beadData-method
> ### plot,beadData,missing-method signalMeans,beadData-method
> ### summary,beadData-method
> ### Keywords: classes
>
> ### ** Examples
>
> data(examplebeadData)
> nGenes(examplebeadData)
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "exprs", for signature "beadData"
Calls: nGenes -> nGenes -> nrow -> exprs -> <Anonymous>
Execution halted
* Installing *source* package 'BeadExplorer' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: widgetTools
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: affy
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: affyio
Loading required package: preprocessCore
Loading required package: R2HTML
Loading required package: tkWidgets
Loading required package: DynDoc
** help
Note: removing empty section \usage
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \usage
Note: removing empty section \details
Note: removing empty section \examples
Note: unmatched right brace in 'beadData-class' on or after line 61
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \note
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \note
Note: removing empty section \examples
Note: removing empty section \note
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \note
Note: unmatched right brace in 'readQC' on or after line 23
Note: unmatched right brace in 'scatterPlot' on or after line 44
>>> Building/Updating help pages for package 'BeadExplorer'
Formats: text html latex example
HumRef8v1 text html latex
HumWG6v1 text html latex
addManifest text html latex example
batchAnalysis text html latex example
beadAnalysis text html latex example
beadData-accessor text html latex
beadData-class text html latex example
beadQC-class text html latex example
boxplotArrays text html latex example
boxplotQC text html latex example
clusterplot text html latex example
cutoff text html latex example
detectionCalls text html latex example
dotplotArrays text html latex example
dotplotQC text html latex example
examplebeadData text html latex example
examplebeadQC text html latex example
extract text html latex example
filterData text html latex example
getAnnot text html latex example
getArrayStats text html latex example
getDet text html latex example
getExprs text html latex example
getID text html latex example
getQC text html latex
getQC2 text html latex
htmloutput text html latex
multiDensity text html latex example
multiecdf text html latex example
normalise text html latex example
pc text html latex example
plotSamples text html latex example
readBead text html latex example
readManifest text html latex example
readQC text html latex example
scatterPlot text html latex example
write.beadData text html latex example
writeQC text html latex example
** building package indices ...
* DONE (BeadExplorer)