[Bioc-devel] Error in Biobase docs

[Seth Falcon]

Keith Satterley <keith at wehi.EDU.AU> writes:

> 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".

Thanks for the report.  I think the fix is:

--- a/Biobase/inst/doc/BiobaseDevelopment.Rnw
+++ b/Biobase/inst/doc/BiobaseDevelopment.Rnw
@@ -96,6 +96,7 @@ Key features in the redesign.
 
 \section{A quick tour}
 <<Biobase,echo=FALSE,results=hide>>=
+options(width=69)
 library(Biobase)
 @ 

> 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 
> error:
> "updateObject(experimentData(+ annotation = updateObject(annotation(object)))"
> I can see this is meant to be
> "updateObject(experimentData),
> + 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.

Certainly a doc bug, but the code is fine (which is why the package
passes R CMD check).

I've committed a fix in devel and we'll port it to the release soon.

+ seth