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wrapping qvalue in Galaxy

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wrapping qvalue in Galaxy

Christophe Antoniewski
Hi,

I am trying to wrap the qvalue R package in a script (as I have already done for a dozen), but this time I have repeatedly the same error
"In fun(libname, pkgname) : no DISPLAY variable so Tk is not available"
or "Loading Tcl/Tk interface ... done" (and red, desperately red box).

I already had this type of bugs and fixed them by using the suppressWarnings or suppressMessages R methods. But this time, no way.
I really don't need the Tcl/Tk interface and I am not using it with qvalue... frustrating. (my code run into R in command lines like a charm)

Any clue to shut off Galaxy and get this miserable pvalue vector output ?


Christophe

PS. I browsed the net, found traces of problems similar to mine, but unfortunately no trace of solutions.

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Re: wrapping qvalue in Galaxy

Ross-2
This is probably because R on a server requires an X11 framebuffer
since your process is not able to open an X11 server connection while
it's running.
Does http://stackoverflow.com/questions/1710853/how-to-run-r-on-a-server-without-x11-and-avoid-broken-dependencies
help?



On Thu, Jun 7, 2012 at 8:57 AM, Christophe Antoniewski
<[hidden email]> wrote:

> Hi,
>
> I am trying to wrap the qvalue R package in a script (as I have already done
> for a dozen), but this time I have repeatedly the same error
> "In fun(libname, pkgname) : no DISPLAY variable so Tk is not available"
> or "Loading Tcl/Tk interface ... done" (and red, desperately red box).
>
> I already had this type of bugs and fixed them by using the suppressWarnings
> or suppressMessages R methods. But this time, no way.
> I really don't need the Tcl/Tk interface and I am not using it with
> qvalue... frustrating. (my code run into R in command lines like a charm)
>
> Any clue to shut off Galaxy and get this miserable pvalue vector output ?
>
>
> Christophe
>
> PS. I browsed the net, found traces of problems similar to mine, but
> unfortunately no trace of solutions.
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/



--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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