[BioC] maQualityPlots on Mac

Herve Pages hpages at fhcrc.org
Wed Aug 30 22:53:34 CEST 2006


Monnie, Rob,

No need to make this discussion private. Other BioC users might benefit
from it.
Cheers,

H.


Rob J Goedman wrote:
> Hi Monnie,
>
> Can you try to start X11 (e.g. from the R Console). PNG needs X11 to
> be running.
>
> Rob
>
>
> On Aug 30, 2006, at 9:29 AM, McGee, Monnie wrote:
>
>> Dear Herve and Rob,
>>
>> I sent the following to the list, but, since you are the ones who
>> answered my last Mac question, I thought you might be able to answer
>> this one, too.
>>
>> Thanks,
>> Monnie
>>
>> Monnie McGee, Ph.D.
>> Assistant Professor
>> Department of Statistical Science
>> Southern Methodist University
>> Ph: 214-768-2462
>> Fax: 214-768-4035
>>
>>
>>
>> -----Original Message-----
>> From: McGee, Monnie
>> Sent: Wed 8/30/2006 11:27 AM
>> To: bioconductor at stat.math.ethz.ch
>> Subject: maQualityPlots on Mac
>>
>> Dear List,
>>
>> I am running R 2.3.1 on a Power Mac G5 with MAC OS 10.4.7 installed. 
>> I am running R from the Cocoa GUI.
>>
>> I tried using the package arrayQuality with the swirl zebrafish data,
>> as outlined in the marray Quick start guide.  I received the
>> following error as I was working along:
>>
>>> maQualityPlots(mraw)
>> Error in X11(paste("png::", filename, sep = ""), width, height,
>> pointsize,  :
>>     unable to start device PNG
>> In addition: Warning message:
>> unable to open connection to X11 display ''
>>
>> So I tried:
>>
>>> maQualityPlots(mraw,dev="jpeg")
>> Error in X11(paste("jpeg::", quality, ":", filename, sep = ""),
>> width,  :
>>     unable to start device JPEG
>> In addition: Warning message:
>> unable to open connection to X11 display ''
>>> maQualityPlots(mraw,dev="ps")
>> [1] "Format error, format will be set to PNG"
>> Error in X11(paste("png::", filename, sep = ""), width, height,
>> pointsize,  :
>>     unable to start device PNG
>> In addition: Warning message:
>> unable to open connection to X11 display ''
>>> maQualityPlots(mraw,dev="quartz")
>> [1] "Format error, format will be set to PNG"
>> Error in X11(paste("png::", filename, sep = ""), width, height,
>> pointsize,  :
>>     unable to start device PNG
>> In addition: Warning message:
>> unable to open connection to X11 display ''
>>>
>>
>> Other graphics, like image() and plot(), run just fine.
>>
>> Incidentally, I tried running maQualityPlots using my X11 version of
>> R, and the option dev="jpeg".  I got the plots that I wanted.  The
>> function also ran with the default device (png), but my Mac could not
>> open the files when I tried to display them.
>>
>> So, I have the devices on my computer ( at least, I have jpeg - but
>> I'd like png, too.  I think the quality would be better), but the GUI
>> interface cannot find it.
>>
>>  How do I get the correct device installed on my Mac and get the GUI
>> to recognize it?
>>
>> Thanks,
>> Monnie
>>
>>
>> Monnie McGee, Ph.D.
>> Assistant Professor
>> Department of Statistical Science
>> Southern Methodist University
>> Ph: 214-768-2462
>> Fax: 214-768-4035
>>
>>
>


-- 
------------------------
Hervé Pagès
E-mail: hpages at fhcrc.org
 Phone: (206) 667-5791
   Fax: (206) 667-1319



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