Re: [Rd] Source references from the parser

From: Seth Falcon <sfalcon_at_fhcrc.org>
Date: Tue 28 Nov 2006 - 00:56:30 GMT

Hi Duncan, all,

Duncan Murdoch <murdoch@stats.uwo.ca> writes:
> This is now committed.
>
> I used keep.source, exactly the same as the option() that controls this
> behaviour in other places.
>
> I decided to set the default to TRUE. This means vignettes will all
> look different in R-devel.

I'd really like the default to be FALSE, at least for the upcoming release. As you note, the change will cause vignettes to look different. There are over 260 vignettes in the BioC source tree and given that most developers have little extra time, I would rather they not have to review these docs because of this change.

> The simplest way to get the previous
> appearance is to put in
>
> \SweaveOpts{keep.source=FALSE}
>
> but in most cases I think people will want the new behaviour. It's only
> bad if the code was badly formatted or contained comments you don't want
> to show up in the final document.

I'm glad the feature is there, I think it is desirable. I hope to turn this option on when I write new documents ;-)

+ seth



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