[BioC] Installation Problems

[Steve Lianoglou]

Hi Rishi,

On Thu, May 23, 2013 at 1:04 PM, Rishi Sinha [guest]
<guest at bioconductor.org> wrote:
>
> Hello!
>
> I was recently just trying to install bioconductor using the source() and then biocLite() commands, but the only problem was that it wasn't able to access:
>
> "http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15"

What do you mean "install bioconductor"? What packages are you trying
to install? Can you show us the `biocLite(...)` command you are using?

If  you are not trying to install the custom CDFs that the brainarray
people provide, then you have no problem. If you look closely at the
message that is being printed, it is only issuing a warning, but you
can carry on with your business.


> Upon going to "http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/", I found that the v2.15 has been removed and only v3.0 is there now.
>
> To download that, how should I change the commands? Or will you guys update it soon?

What is "that" that you want to download? If you really want to access
older versions of their custom CDFs, you can browse what they have
here:

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp

If worse comes to worst, you can download the package you want and
install manually from the local package.

> Also, after using biocLite(), it prompts me about whether I would like to update all/some/none packages (a/s/n), but it doesn't respond to any inputs ('a', 'all', etc.) and I'm forced to quit it using 'esc'. Any idea what the problem might be??

I haven't experienced that before (but I've also never run R on
windows). How are you running R? Are you, for instance, using rstudio,
emacs/ess, or?

-steve

--
Steve Lianoglou
Computational Biologist
Department of Bioinformatics and Computational Biology
Genentech