[BioC] maQualityPlots on Mac

[Marcus Davy]

Have you installed the X11.app from the tiger/panther installation disks?

The X11.app needs to be running in conjunction with R to then access the X11
graphics. I believe quartz() doesn't need X11.app to work.

Also, I make a Rprofile.site file to store global options in R_HOME$/etc,
For a system level install, it goes somewhere like;

/Library/Frameworks/R.framework/Versions/Current/Resources/etc

First <- function() {
 Sys.putenv("DISPLAY"=":0")       # <----- this may be your problem too
 Sys.putenv("http_proxy"="http://[YOUR PROXY]:[PORT]")
 options(device="X11")
}


Marcus

On 8/31/06 8:53 AM, "Herve Pages" <hpages at fhcrc.org> wrote:

> 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
>>> 
>>> 
>> 
> 


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