[BioC] biocLite() fails to install all limma dependencies from CRAN

[Seth Falcon]

"Gordon K Smyth" <smyth at wehi.EDU.AU> writes:

> Hi Jenny,
>
> statmod is deliberately a "suggests" rather than a "depends" because
> only a small number of limma functions use it.
>
> As far I remember, there the Bioconductor install behaviour hasn't
> changed.  Maybe I misremember, but I don't think biocLite() has ever
> installed suggested packages from CRAN.

biocLite has not changed its behavior for this release.  However, you
can use biocLite to install Suggests.  Here are a couple ways to do
this:

   biocLite("limma", dependencies=c("Depends", "Suggests", "Imports"))

or simply

   biocLite("limma", dependencies=TRUE)

This has one slight downside: install.packages will install the
Suggests for all Depends not just the package you asked for.  So you
can end up getting many more packages than you really need.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org