[BioC] arrayQualityMetrics run as batch-job: unable to start device PNG - SOLVED!

[Knut Hansen]

I found that if I include the line:
options(bitmapType="cairo")
in my R-script everything works fine!

Knut

Den 13. nov. 2012 18:06, skrev Wolfgang Huber:
> Hi Knut
> 
> if James' pointers do not help, can you please send an example script that reproduces the error and the output of sessionInfo. This type of matter is very system- and version-dependent.
> 
> 	Best wishes
> 	Wolfgang
> 
> Il giorno Nov 13, 2012, alle ore 3:58 PM, James W. MacDonald <jmacdon at uw.edu> ha scritto:
> 
>> Hi Knut,
>>
>> On 11/13/2012 7:14 AM, Knut Hansen wrote:
>>> Hi,
>>>
>>> I'm trying to run a R-script which calls arrayQualityMetrics as a
>>> batch-job on a remote machine. But I get the error message:
>>> Error in X11(paste("png::", filename, sep ="), g$width, g$height,
>>> pointsize,  :
>>>   unable to start device PNG
>>
>> See R FAQ 7.19 (http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-do-I-produce-PNG-graphics-in-batch-mode_003f)
>>
>> Best,
>>
>> Jim
>>
>>
>>>
>>> The script runs fine if I run it interactively from the command line.
>>>
>>> A bit of googleing tells me that this may have to do with the R png
>>> device which needs the X11 device.
>>>
>>> Does anybody have any hints on how I can solve this?
>>>
>>> Knut Hansen
>>>
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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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> 
>