[BioC] Problems using arrayQualityMetrics

[Syed Haider]

Dear Wolfgang,

Ros's computer definitely needs an upgrade. However, looking breifly 
into this, here is the offending line of code from 
arrayQualityMetrics::aqm.report.qm(...)

size = annotateSvgMatplot(svgtemp, nameimg, annotationInfo=qm$svg)

The above fails while generating pca.svg and rnadeg.svg. Interestingly 
density.svg comes out *okish*. The density plot looks correct but 
without axis-labels and legends. All other figures are fine too, 
including the pdf equivalent of all svgs.


Best,
Syed


On 22/03/2012 23:39, Wolfgang Huber wrote:
> Dear Rosalind
>
> unfortunately, the fact that the package manager on your Redhat Linux
> does not provide you with a newer version does not mean that there is
> none. The Linux distribution that you are using seems to be very much
> behind in time: cairo 1.2.4 is from 2006, see http://cairographics.org/
>
> Two options:
> - use a system that is better kept up-to-date
> - remove the cairo that your package manager gives you, and install
> libcairo >=1.10.2 'manually' by downloading it from the above URL.
>
> Btw, I would also also prefer if arrayQualityMetrics (i.e., really the
> SVGAnnotation package) was backwards compatible with any old version of
> cairo, but that is not a realistic expectation (neither for our
> software, nor for many other products, incl. commercial).
>
> Best wishes
> Wolfgang
>
> Mar/22/12 12:38 PM, Rosalind Cutts scripsit::
>> Thanks very much for the reply, I have tried this with a clean R and
>> bioconductor installation and get a similar error.
>>
>> ArrayQualityMetrics works ok, it just fails to produce some of the
>> graphical output.
>>
>> Cairo version:
>> pkg-config --modversion cairo
>> 1.2.4
>>
>> When I tried updating Cairo on the Redhat linux machine I am using as
>> suggested by your link there were no updates to load.
>>
>> Is there anything else that you could suggest I could try.
>>
>> Thanks again for your help
>>
>> Ros
>
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
>
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