[R-SIG-Mac] Outdated links to the Bioconductor repos in R.app

Seth Falcon sfalcon at fhcrc.org
Wed May 24 15:47:04 CEST 2006

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

> Herve,
> 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 ;)).
>> 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? This will list all packages, even  
> non-Bioc ones in the package selection. Maybe it should be handled  
> separately (e.g. added on installation, but omitted when available  
> packages are listed?).

Many Bioc packages depend on packages hosted on CRAN.  What is needed
is that _some_ CRAN repository be in the vector of repositories
specified by the 'repos' argument in calls to install.packages and
update.packages.  Otherwise, dependencies won't be installed.

If there is a way to handle this separately so that CRAN packages
don't come up in a Bioc listing, that seems like an improvement to me.

And to be clear, we've put our (FHCRC) CRAN mirror there not because
we think that is the best solution, but because it works.  A planned
improvement is to try and detect the current repos option and only add
if needed.

>> 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 ;)).

Hmm, I wonder if we need to have a vote on bioc-devel :-)

Best Wishes,

+ seth

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