I have run into this issue yesterday with another package.  There is an as
yet unidentified problem with installability of current images of some
packages in the devel branch.  It has been pointed out that the windows
binary for rtracklayer

(see http://bioconductor.org/packages/2.10/bioc/html/rtracklayer.html )

is of much earlier vintage than that for other platforms, as it has not
been passing check on windows for some time.  This could lead to the sort
of behavior seen here.  I will be looking at the port to windows later
today, and will share relevant news.

On Thu, Feb 16, 2012 at 6:45 AM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> On Thu, Feb 16, 2012 at 6:29 AM, Bernd Jagla <bernd@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
>
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