[R-SIG-Mac] Outdated links to the Bioconductor repos in R.app

[Simon Urbanek]

On May 24, 2006, at 4:40 PM, Herve Pages wrote:

> Kasper Daniel Hansen wrote:
>>> I don't. There may be others as well... I'd rather BioC
>>> packages be kept separate from CRAN packages in the
>>> listing...
>>
>> I second that. While I am indifferent to what goes on under the hood,
>> the Gui (as it stands right now) should only list Bioconductor
>> packages when selecting either "Bioconductor (sources)" or
>> "Bioconductor (binaries)".
>
> OK so ideally the GUI should use 2 sets of repos:
>
>   - one for _displaying_ the list of Bioconductor packages:
>
>       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
>
>     NB: Note that having omegahat and lindsey will help to prevent
>     questions like "Hey my package xxx says it depends on SSOAP but
>     I don't see SSOAP in the list and it's not in CRAN neither!".
>     Having omegahat and lindsey adds less than 10 packages anyway...
>
>   - one for _installing_ the selected packages:
>
>       same as above + http://cran.fhcrc.org
>
> And the installation should be done with 'dep=TRUE'.
>

As of dep=TRUE - that is what the "install dependencies" checkbox is  
about. And yes, the above was my proposal and the responses seem to  
confirm it. I have now modified the PI such that the list will be  
based on "BioC.repos" and installation will add "repos" (revision 3178).

Cheers,
Simon