[Bioc-devel] Error in Biobase docs

Keith Satterley keith at wehi.EDU.AU
Tue Oct 17 05:25:17 CEST 2006

To Biobase authors, in particular Martin Morgan,

I was looking at Vignette no. 2 in the Biobase package which displays a pdf 
entitled "Biobase development and the new eSet"
The author is Martin T. Morgan, and it is dated 7 August, 2006 and the revision 
text is "Revised 4 September, 2006 – featureData slot".

On Page 11 of this document, you have

and add code to update to the new version
 > setMethod("updateObject", signature(object = "MySet"), function(object,
+ ..., verbose = FALSE) {
+ if (verbose)
+ message("updateObject(object = MySet )")
+ object <- callNextMethod()
+ if (isCurrent(object)["MySet"])
+ return(object)
+ if (!isVersioned(object))
+ new("MySet", assayData = updateObject(assayData(object)),
+ phenoData = updateObject(phenoData(object)), experimentData = 
updateObject(experimentData(+ annotation = updateObject(annotation(object)))
+ else {
+ classVersion(object)["MySet"] <- classVersion("MySet")["MySet"]
+ object
+ }
+ })
[1] "updateObject"

One doesn't see the error in the pdf as it is past the right margin. When copied 
and pasted into an R console there is an error message because of the following 
"updateObject(experimentData(+ annotation = updateObject(annotation(object)))"
I can see this is meant to be
+ annotation = updateObject(annotation(object)))"

Perhaps another line break before "experimentData =" in the line before this 
would also avoid the text going beyond the right margin.

Thanks for all the work you put into R package development,

 > sessionInfo()
R version 2.4.0 (2006-10-03)


attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils" 
"datasets"  "base"

other attached packages:



Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia

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