[BioC] arrayQualityMetrics not producing all diagnostic plots

[James F. Reid]

Wolfgang Huber <whuber at ...> writes:

> 
> Hi James,
> 
> 1.) the "length(annotationInfo$annotation)" complaint is (as far as I 
> currently understand it) related to a version incompatibility between 
> newer versions of libcairo on your computer and the SVGAnnotation 
> package. I am working with Duncan to sort this out. (See also 
> https://stat.ethz.ch/pipermail/bioconductor/2010-October/035958.html)
> 
> What is the output of:
>     pkg-config --modversion cairo
> on both of your machines?

Hi Wolfgang,

on the machine with the length complaint I have 1.10.0 and on the machine with
the XML-node complaint I have 1.2.4.

Thanks.
James.


> 
> 2.) I have never seen the other error you report (about something being 
> NULL that should be an XML-node), but it smells like it could be a 
> consequence of the same underlying problem: format or content of an SVGH 
> graphics file (which is an XML document) that is not expected by 
> SVGAnnotation.
> 
> I am sorry that this functionality is so brittle. When it works, it is 
> great, see e.g. 
>
http://www-huber.embl.de/users/whuber/arrayQualityMetrics-Reports/CCl4-RIN/QMreport.html

> Figures 4, 6 and 
>
http://www-huber.embl.de/users/whuber/arrayQualityMetrics-Reports/MLL/QMreport.html 
> Figs. 4, 6, 8. I am working right now on making it more robust!
> 
> For now, all I can offer is the workaround already suggested in the 21 
> Oct post. Sorry for that, this seems to be the cost of being 'cutting-edge'.
> 
> 	Best wishes
> 	Wolfgang
>