[BioC] biocLite and limma

James W. MacDonald jmacdon at med.umich.edu
Wed Jun 29 18:22:26 CEST 2011

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.



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