[BioC] qrqc with error message of "unable to start device PNG" and "unable to open connection to X11 display"?

[Dan Tenenbaum]

Hi SangChul and Jim,

On Wed, May 30, 2012 at 6:22 AM, James W. MacDonald <jmacdon at uw.edu> wrote:
> Hi SangChul,
>
>
> On 5/29/2012 4:46 PM, Sang Chul Choi wrote:
>>
>> Hi,
>>
>> I am trying to use qrqc Bioc package in a linux machine used as a compute
>> node.  I have the following error:
>>
>> ====================
>> Error in X11(paste("png::", filename, sep = ""), g$width, g$height,
>> pointsize,  :
>>   unable to start device PNG
>> In addition: Warning message:
>> In grDevices::png(..., width = width, height = height, res = dpi,  :
>>   unable to open connection to X11 display ''
>> ====================
>>
>> I have googled for an answer and bumped into following mailing list posts:
>>
>> https://stat.ethz.ch/pipermail/r-help/2008-March/155943.html
>> https://stat.ethz.ch/pipermail/r-help/2008-February/155021.html
>> https://stat.ethz.ch/pipermail/r-help/2008-February/155023.html
>>
>> It is not obvious what I should do. I will appreciate your answers.
>
>
> The simple answer is to run the code on the head rather than a compute node.
> In my experience, compute nodes usually don't have 'GUI-type' software
> installed (X11, png, etc), as it is not common for people to need that sort
> of thing.
>

If Jim's suggestion to run the relevant computations on your Windows
machine does not work out, you can go back on the Linux machine and
start R. What is the output of the
capabilities()
command?
And
sessionInfo()
for that matter?

Can you tell what the exact command is that causes the error?
Do you need your files to be in png format?

If you install the Cairo package:
biocLite("Cairo")

Does qrqc then work?
Is it practical to use bitmap() to generate your png?

What Linux distribution are you on? You may want to install Xvfb which
should solve the problem, though it can be sort of tricky, according
to this somewhat dated page for Ubuntu.
http://blog.martin-lyness.com/archives/installing-xvfb-on-ubuntu-9-10-karmic-koala

Dan




> Best,
>
> Jim
>
>
>
>>
>> Thank you,
>>
>> SangChul
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>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
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