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

Wolfgang Huber huber at ebi.ac.uk
Tue Dec 5 16:27:02 CET 2006

Hi all,

Seth wrote:
> I like the idea of being able to modify SweaveOpts without having to
> change the vignette contents.  For this to be usable for us, it needs
> to get picked up by 'R CMD build', at least, because that is how
> vignettes get built in our build system.
> A central BiocSweaveDefaults.Rnw file could be more trouble than it is
> worth.  It requires modifying all vignettes to include the file and
> then there is the question of where such a file would live.
> Generally, developers only maintain a single package and don't do a
> checkout of everything.  Right now, packages are self-contained and I
> would hate to see that change.  -- but I think something along these
> lines could provide useful insulation against changes in Sweave that
> we aren't ready for.

This discussion seems to move into the direction of having different
"flavours" of R. In addition to --vanilla, we could add a --bioc
flavour. Alternatively, a really minimal "Biobase"-type package that
needs to be loaded for any use with Bioconductor and contained such
goodies as setting the Sweave default behaviour and the biocLite script?

I am not sure whether this a direction that we really want to take, and
I am here not suggesting actually taking it, but isn't this the logical

 Best wishes

Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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