[Bioc-devel] sma and your Bioconductor package

[Gordon K Smyth]

limma and limmaGUI have been suggesting sma until now because we have be 
using a microarray dataset contained in it for examples.  We don't use any 
sma code for funtionality.

We have already taken steps to remove sma from the suggests list of limma.

Best wishes
Gordon

On Sat, 26 Sep 2009, Martin Morgan wrote:

> aCGH: Depends
> GeneSelector: Suggests
> limma: Suggests
> limmaGUI: Suggests
> MLInterfaces: Suggests
>
> sma: http://cran.r-project.org/src/contrib/Archive/sma/sma_0.5.15.tar.gz
>
> Package maintainers --
>
> As you may know, 'sma', has been removed from CRAN. This means that the
> functionality of your package that depends on sma WILL NOT WORK for any
> new user of your package.
>
> Please respond on the Bioc-devel mailing list, or to this email, about
> how you'd like to deal with this. Possibilities include:
>
> a) sma was non-essential, my package code will be adjusted to work
> around this
>
> b) there is some core functionality in sma that could be extracted and
> incorporated in my package / another existing package. If this is the
> case it would be good to hear what that code is (and where it might go).
> Vince has already pointed to sma::stat.diag.da
>
> c) sma is essential, it should be incorporated into Bioconductor.
>
> Martin
> -- 
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793