[BioC] arrayQualityMetrics not producing all diagnostic plots

[James F. Reid]

Dear all,

Since upgrading to the latest version of Bioconductor, I am having 
problems using the package arrayQualityMetrics because it does not 
produce a full report (both for single and double channels arrays).

Thanks.
James.

Here is the first example from the arrayQualityMetrics vignette 
(inst/scripts/arrayQualityMetrics.Rnw)

library("ALLMLL")
data("MLL.A")

library("arrayQualityMetrics")
arrayQualityMetrics(expressionset = MLL.A,
                     outdir = "MLL",
                     force = TRUE,
                     do.logtransform = TRUE)

produces:
Error in UseMethod("xmlAttrs", node) : no applicable method for 
'xmlAttrs' applied to an object of class "NULL"

without producing all the plots (stops after section 3: Between array 
comparison), the html report is truncated.

 > sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] ALLMLL_1.2.8              arrayQualityMetrics_3.2.0
[3] vsn_3.17.2                affyPLM_1.25.1
[5] preprocessCore_1.11.0     gcrma_2.21.1
[7] affy_1.27.3               Biobase_2.9.2

loaded via a namespace (and not attached):
  [1] affyio_1.17.4         annotate_1.27.3       AnnotationDbi_1.11.10
  [4] beadarray_2.0.1       Biostrings_2.17.48    DBI_0.2-5
  [7] genefilter_1.31.2     grid_2.12.0           hwriter_1.2
[10] IRanges_1.7.40        lattice_0.19-13       latticeExtra_0.6-14
[13] limma_3.5.21          marray_1.27.0         RColorBrewer_1.0-2
[16] RSQLite_0.9-2         simpleaffy_2.25.0     splines_2.12.0
[19] stats4_2.12.0         survival_2.35-8       SVGAnnotation_0.6-0
[22] XML_3.2-0             xtable_1.5-6
 >