[R-SIG-Mac] Outdated links to the Bioconductor repos in R.app

[hpages at fhcrc.org]

Quoting Simon Urbanek <simon.urbanek at r-project.org>:

> On May 23, 2006, at 10:31 PM, Herve Pages wrote:
> 
> > I'm using R.app GUI 1.16-pre (3114) with R 2.3.0.
> > The links defined in R.app for accessing the Bioconductor  
> > repositories need to be updated.
> >
> 
> This has been fixed in 3161 (and of all the people you should know,  
> actually ;)).

Simon,

Point taken. In the future, I'll try to base my reports on the last
Mac OS X GUI available here http://r.research.att.com/#GUI

> 
> > but they should be (in this order):
> >
> >    http://bioconductor.org/packages/bioc
> >    http://bioconductor.org/packages/data/annotation
> >    http://bioconductor.org/packages/data/experiment
> >    http://bioconductor.org/packages/omegahat
> >    http://bioconductor.org/packages/lindsey
> >    http://cran.fhcrc.org
> >
> 
> Should CRAN be really on that list?

Well it depends what you are trying to achieve: if you want the GUI
to show the user the list of Bioconductor packages only, then you
don't need the 3 last repos.
But if you also want the user to be able to install from this list and
then to load the newly installed stuff, then you need 2 things:

  1) provide a set of repos that is closed for the dependency relationship

  2) provide the user with the option to have all the dependencies
     installed in addition to the packages s/he selected

Since the GUI doesn't support 2), then I agree that we don't really
need the 3 last repos (omegahat, lindsey and CRAN)... But I'd rather
keep them anyway because:

  - Some users might want to do things like:
      install.packages('pkg', repos=getOption("BioC.Repos"), dep=TRUE)
    The only way to guarantee that this will work for _any_ Bioconductor
    package is to have all 5 repos returned by getOption("BioC.Repos")

  - Things are consistent with the biocLite() function that we provide
    for users of _all_ platforms
      http://bioconductor.org/docs/install-howto.html

The inconvenient of this is that we end up with the GUI displaying a very
long list... but this is not really a problem because I don't think many
users actually browse the entire list: they'd rather use the search box
instead.

> Lindsey was omitted intentionally, because the packages are  
> constantly broken (0 of them compile on OS X to-date) and the  
> maintainer refuses to fix them despite instructions how to do so.  
> (His last response was that the users should fix it themselves...)

That's sad :-/

> > Also, we have started to use a more consistent spelling for the  
> > project ( it's never too late ;-) ): please help us by using  
> > "Bioconductor" instead of "BioConductor".
> >
> 
> Oh, ok :). Are we allowed to use BioC or is it also Bioc? (The latter  
> looks rather boring ;)).

Agreed :-), but OTOH, as Seth told me recently, "BioC" might suggest that
we are using C instead of R.
Anyway, let's stick to "BioC" for now...
Thanks!

H.