[BioC] problem with Gviz installation...

[Steve Lianoglou]

Hi,

On Thu, Feb 16, 2012 at 6:29 AM, Bernd Jagla <bernd at pasteur.fr> wrote:
> Hi,
>
> I have to agree that after reading the vignette it seems all my question
> might have been answered... or are pretty close to being answered... THANKS
> A LOT for your continued support.
>
> Unfortunately I am having problems right now to use Gviz with my windows
> system... I am running into the following error message and don't know how
> to resolve this problem:
>
>
>> library(Gviz)
> Error : Klassen '"file", "connection"' sind nicht von 'namespace:IRanges'
> exportiert
> Fehler: Laden von Paket/Namensraum für ‘Gviz’ fehlgeschlagen
>
> Maybe someone can help me there???
>
> Just for translation and what I understood: the classes file and connection
> are not defined in the namespace IRanges but are defined in base... I don't
> know how to unload base and if it is possible/useful to do so... or how to
> overwrite them...

Hmmm ... actually, these classes should be currently exported from
BiocGenerics, but at one point they were defined in IRanges (before
BiocGenerics was born).

If I understand the German correctly (fat chance), it seems you have
an older version of *some* package that is trying to import these
classes from IRanges when it should really be grabbing them from
BiocGenerics -- the strange thing is that I have slightly older
versions of the same packages you are showing (still on
R-devel/bioc2.10 though) and the install works for me.

Did you install Gviz via biocLite?

Maybe you can try updating your installed packages and try again, like so?

The following commands will update all packages on your system w/o
asking you to confirm [y/n] each one:

library(BiocInstaller)
biocLite(character(), ask=FALSE)

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact