[Bioc-devel] Sweave changes (keep.source = TRUE or FALSE?)

[Friedrich Leisch]

>>>>> On Tue, 05 Dec 2006 15:23:24 -0500,
>>>>> Duncan Murdoch (DM) wrote:

  > Right, that's what we want to do.  But I want an easier way for someone 
  > with an existing document to get the old behaviour.


My plan would be the following:

1) Set the default of all Sweave options via options(), such that it
   can be changed in the Rprofile of a site-wide installation or in a
   user's ~/.Rprofile file or even on a per-directory basis. This will
   also result in R CMD build reading the desired defaults.

2) Have something like
	R CMD Sweave --opts "additional args passed to Sweave() call"
   to be able to override it even from the shell.

If BioC decides to default to keep.source=FALSE and stylepath=TRUE
then it will not be necessary to touch any existing vignettes. R CMD
check and build currently run R --vanilla and hence ignore the stuff in
1), so will need changes there, too. But nothing that's not doable,
I'll give it a shot over Christmas break. 

Best,
Fritz