[BioC] new arrayQualityMetrics 3.2.3 in release - was: arrayQualityMetrics 3.2.0 in Bioc release 2.7 is broken

[Wolfgang Huber]

Dear Bioconductors

arrayQualityMetrics_3.2.3 is now available from the release branch. To 
update your existing version, what you need to do is run

   source("http://bioconductor.org/biocLite.R")
   update.packages(repos=biocinstallRepos(), ask=FALSE, checkBuilt=TRUE)

in R-2.12. It fixes two issues that were discussed on this list recently:

1. Incompatibility between the R package SVGAnnotation_0.7-0 and the 
system library libcairo 1.10 (Duncan has recently released 
SVGAnnotation_0.7-2, on which arrayQualityMetrics now depends).

2. Overzealous error throwing for some Affymetrix genechip datasets that 
have no MMs, as was recently noted by Tim 
(https://stat.ethz.ch/pipermail/bioconductor/2010-November/036372.html).

	*	*	*

One thing to note: SVGAnnotation does not work with very old versions of 
libcairo. If you run into this, you'll either need to update your 
libcairo, or also use an old version of arrayQualityMetrics.

Btw, more interactivity enhancements are under way for 
arrayQualityMetrics in the current devel branch - but this is not yet 
fit for production use and will need a few more weeks.

	Best wishes
	Wolfgang


Il Oct/21/10 10:40 AM, Wolfgang Huber ha scritto:
>
> This will manifest itself by seeing the error message
>
> Error in aqm.highlight(doc, annotationInfo = annotationInfo) :
> 'length(annotationInfo$annotation)' must be equal to 'length(series)',
> the number of objects in the plot.
>
> The reason appears to be a misfit between R's SVG-device and the package
> SVGAnnotation that seems to have entered just a few days before
> R-2.12.0's release. I am working on a solution and will announce it here.
>
> As a workaround until then, please use
> http://www.bioconductor.org/packages/2.6/bioc/html/arrayQualityMetrics.html
> (For R-2.12 users: first install the package as usual with "biocLite",
> then manually download the version above and install it over that.)
>
> Sorry for the trouble.
>
> Best wishes
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
>
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