[BioC] biocLite and limma

[James W. MacDonald]

Hi Naomi,

Please start a new thread, rather than responding to an existing thread 
and simply changing the subject line. For those of us using a 
thread-aware email client, this appears to be part of the '2 way anova 
in Bioconductor' thread.

On 6/29/2011 12:01 PM, Naomi Altman wrote:
> statmod does not get installed along with limma. Even if I install
> statmod manually, it does not load when limma is loaded (although it
> does when it is needed). This problem has persisted for several
> generations of limma.

This isn't a problem, it is a feature. The statmod package is listed as 
a suggested package, rather than a dependency, so it won't be installed 
by default, nor will it be loaded by default.

Suggested packages are those that are not critical to the functionality 
of a package, but that can extend functionality in certain 
circumstances. Since statmod is only used in cases where end users 
choose to fit mixed models (likely a fairly rare event, and done so by 
more sophisticated users), listing statmod in suggests reduces downloads 
and loading of something not likely to be useful for the average limma user.

Best,

Jim


>
> --Naomi
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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