Hi,

 Not that I am likely to add anything new here. I think among the many
problems I have with changing the default behavior is the impact it has on
BioC developers, authors that have relied on the current behavior as has the
bioc developement system.  Fritz and Duncan's proposal involves a lot of
work for us. More than 200 documents need to either be hand checked to see
if the new behavior is fine or have keep.source=FALSE added to them. Since
the latter route is easier I suspect it will be the one taken most often so
there will be lots of work done and none of the so-called benefits. Only
newly written vignettes are likely to use keep.source=TRUE, and we could get
all those benefits with no changes to current documentation by setting the
default appropriately.

I am concerned that the R package system will not support such arguments and
then the Bioc build system will be forced to either ship broken
documentation or be retooled so that we essentially end up by-passing the
entire vignette building code in the R package system (R CMD build and
friends) and that is an even worse situation for not testing code, IMHO. And
I share some of Laurent's concerns - but if we need to, we can just build
our own code for doing many of these things - it would just be nice not to
be forced down that road.

 best wishes
  Robert



On 12/5/06, lgautier@altern.org <lgautier@altern.org> wrote:
>
> > 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
> >
> > _______________________________________________
> > Bioc-devel@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> _______________________________________________
> Bioc-devel@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>


-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem@fhcrc.org

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