[galaxy-dev] wrapping qvalue in Galaxy

2012-06-06 Thread 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: [galaxy-dev] wrapping qvalue in Galaxy

2012-06-06 Thread Ross
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
droso...@gmail.com 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.

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

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