I was able to get Gviz installed on an old windows system under R-devel.
The trick was to install current rtracklayer from source -- the binary is
still not building owing to an error in an example.  You need the windows
toolset to do this; see the R Installation and Administration manual if
necessary.

> sessionInfo()
R Under development (unstable) (2012-02-16 r58364)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] Gviz_0.1.12          rtracklayer_1.15.7   GenomicRanges_1.7.25
[4] IRanges_1.13.24      BiocGenerics_0.1.4   RCurl_1.91-1.1
[7] bitops_1.0-4.1       BiocInstaller_1.3.7

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.17.21 Biobase_2.15.3        biomaRt_2.11.1
 [4] Biostrings_2.23.6     BSgenome_1.23.2       DBI_0.2-5
 [7] lattice_0.20-0        RColorBrewer_1.0-5    Rsamtools_1.7.33
[10] RSQLite_0.11.1        tools_2.15.0          XML_3.9-4.1
[13] zlibbioc_1.1.1


On Thu, Feb 16, 2012 at 6:56 AM, Vincent Carey
<stvjc@channing.harvard.edu>wrote:

> 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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>>
>
>

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