[R-SIG-Mac] Outdated links to the Bioconductor repos in R.app

[Paul Roebuck]

On Wed, 24 May 2006 Herve Pages wrote:

> Quoting Simon Urbanek <simon.urbanek at r-project.org>:
>
> > On May 23, 2006, at 10:31 PM, Herve Pages wrote:
> >
> > [SNIP]
> >
> > > 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")

Forgive, but if that's the case, why can't it be specified as such:

whole.enchilda.repos <- c(getOption("BioC.Repos"),
                         "http://bioconductor.org/packages/omegahat",
                         "http://cran.fhcrc.org")  # getOption("repos")?
install.packages('pkg', repos = whole.enchilda.repos, depend = TRUE)

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

Since the above would be an internal change to the install
script, the above would be even less effort.

> 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.

I don't. There may be others as well... I'd rather BioC
packages be kept separate from CRAN packages in the
listing...

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