[BioC] arrayQualityMetrics NULL XML-node Error; Anyone still getting this?

[Paniagua, Eric]

Hi Bioconductors (hopefully still including Wolfgang),

I have updated my packages, as per this list's posting guide, but to no avail.  I have also searched the archives, and I discovered this thread where someone had a very similar problem (http://thread.gmane.org/gmane.science.biology.informatics.conductor/31622/focus=31666).  I do not see there any solution.  It's been about a year since that thread circulated, so I was wondering if anyone else has encountered this XML problem when running arrayQualityMetrics.

It is not clear that my error is exactly the same as what James (from the above thread) encountered, but I'm thinking it's likely related.  Maybe there is a parallel code block to the one throwing an error for James that wasn't fixed and is only now being observed.  The differences from James's report follow:

1) I do get sections 4 and 5 in the index.html report file.

2) I have a notice beneath the caption for Figure 3 which reads: "Note: the figure is static - enhancement with interactive effects failed. This is either due to a version incompatibility of the 'SVGAnnotation' R package and your version of 'Cairo' or 'libcairo', or due to plot misformating. Please consult the Bioconductor mailing list, or contact the maintainer of 'arrayQualityMetrics' with a reproducible example in order to fix this problem."

$ pkg-config --version cairo
0.21

$ xml2-config --version
2.6.26

The binary libcairo file installed is at /usr/lib64/libcairo.so.2.9.2

Figures 6 and 12 *are* interactive, which leads me to think it could be either a version mismatch issue between libcairo and SVGAnnotation or a code issue in the arrayQualityMetrics package itself.

I also have another case with the same error manifesting slightly differently, but I figure it's best to have everything working correctly for sample code from the vignette first (http://www.bioconductor.org/packages/2.8/bioc/vignettes/arrayQualityMetrics/inst/doc/arrayQualityMetrics.pdf and below).  I notice that some of my versions are slightly newer than those from the vignette.

Details:
* R was run as: R --vanilla
* R and all packages are installed on a 48-core server, 64-bit, running CentOS 5.5 (final)
* For viewing, I copied the output to my local machine (dual-core laptop running Ubuntu 10.10)
* I viewed index.html in Google Chrome 14.0.835.186

My example R session demonstrating the error follows.

I would greatly appreciate any feedback, suggestions, questions, and/or answers you may be able to provide.

Thanks,
Eric Paniagua

PS: I apologize for the lack of monospace font in what follows; I can't find how to set it in the OWA client.

R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library("ALLMLL")
Loading required package: affy
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

> data("MLL.A")
> library("arrayQualityMetrics")
> arrayQualityMetrics(expressionset = MLL.A[, 1:5],
+                     outdir = "Report_for_MLL_A",
+                     force = TRUE,
+                     do.logtransform = TRUE)
The directory 'Report_for_MLL_A' has been created.
Error in UseMethod("xmlAttrs", node) : 
  no applicable method for 'xmlAttrs' applied to an object of class "NULL"
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
> traceback()
No traceback available 
> warnings()
NULL
> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] hgu133acdf_2.8.0          arrayQualityMetrics_3.8.0
[3] ALLMLL_1.2.8              affy_1.30.0              
[5] Biobase_2.12.2           

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.14.1  Biostrings_2.20.4     Cairo_1.5-0          
 [4] DBI_0.2-5             Hmisc_3.8-3           IRanges_1.10.6       
 [7] KernSmooth_2.23-6     RColorBrewer_1.0-5    RSQLite_0.10.0       
[10] SVGAnnotation_0.9-0   XML_3.4-3             affyPLM_1.28.5       
[13] affyio_1.20.0         annotate_1.30.1       beadarray_2.2.0      
[16] cluster_1.14.0        genefilter_1.34.0     grid_2.13.1          
[19] hwriter_1.3           lattice_0.19-33       latticeExtra_0.6-18  
[22] limma_3.8.3           preprocessCore_1.14.0 setRNG_2009.11-1     
[25] splines_2.13.1        survival_2.36-10      tools_2.13.1         
[28] vsn_3.20.0            xtable_1.5-6