[BioC] GOstats

[Francois Pepin]

Hi Ali

> Thanks for the prompt response.  I thought it might be a versioning
> issue, but I religiously update every Monday AM!
> 
> I use:
> * Windows GUI Menu
> * Melbourne CRAN mirror
> * all 4 repositories.
>
> then run update packages from the menu.   This should do the trick,
> shouldn't it, normally?  

I'm unfamiliar with the windows GUI menu, but the annotation and the
experiment data each have a repository of their own. I'm guessing you're
not in your list. You might want to add them manually, the relevant
lines from the biocLite.R (after sourcing getBioC and biocinstall):

   ## CRAN-style Repositories where we'll look for packages
    repos <- c(
        "bioc",
        "data/annotation",
        "data/experiment",
        "omegahat",
        "lindsey"
    )
    repos <- paste("http://bioconductor.org/packages/1.8", repos, sep="/")
    repos <- c(repos, "http://cran.fhcrc.org")

This isn't recommended though, because it's more error-prone to changes.
biocLite gets updated to make sure it keeps on working as it should
(like verifying that you have the right R version and such).

> is there a way of unloading it from RAM, so that an update can be done
> without restarting the session?

you might want to look at ?detach. I am not familiar enough with the R
internals enough to know if it frees the RAM or not.

Francois