[Rd] Source references from the parser

[Seth Falcon]

Hi Duncan, all,

Duncan Murdoch <murdoch at 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