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

[lgautier at altern.org]

> 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.

I hope this will not happen, as I would suspect this is problem-prone.

>          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?

That would be a much better option, IMHO: settings specific to BioC would
remain separate from R-core.

> 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
> consequence?

I would not see the fact that Biobase would be setting a couple of options
as a novel and dramatic change. In the time 'reposTools' was used, the
default system system for R repositories was completely by-passed, and
bioClite is still something sitting on the top of install.packages
-somehow-... or did I miss something ?


L.



>  Best wishes
>   Wolfgang
>
> --
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>
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