[BioC] arrayQualityMetrics error

[Paulo Nuin]

Hi everyone

We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run.

It goes fine until section 5, were it is interrupted by an error

> arrayQualityMetrics(rawAffyData, outdir="quality", force=T)
The report will be written into directory 'quality'. 
[[1]]

[[2]]

[[3]]

[[4]]

Error in UseMethod("xmlAttrs", node) : 
  no applicable method for 'xmlAttrs' applied to an object of class "NULL"
In addition: There were 39 warnings (use warnings() to see them)

Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated.

Cheers
Paulo

> capabilities()
    jpeg      png     tiff    tcltk      X11     aqua http/ftp  sockets 
    TRUE     TRUE     TRUE    FALSE     TRUE    FALSE     TRUE     TRUE 
  libxml     fifo   cledit    iconv      NLS  profmem    cairo 
    TRUE     TRUE     TRUE     TRUE     TRUE    FALSE     TRUE 



> sessionInfo()
R version 2.12.1 (2010-12-16)
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  methods   base     

other attached packages:
[1] hgu133plus2cdf_2.7.0      arrayQualityMetrics_3.2.4
[3] vsn_3.18.0                affyPLM_1.26.0           
[5] preprocessCore_1.12.0     gcrma_2.22.0             
[7] affy_1.28.0               Biobase_2.10.0           

loaded via a namespace (and not attached):
 [1] affyio_1.18.0        annotate_1.28.0      AnnotationDbi_1.12.0
 [4] beadarray_2.0.3      Biostrings_2.18.2    DBI_0.2-5           
 [7] genefilter_1.32.0    grid_2.12.1          hwriter_1.3         
[10] IRanges_1.8.8        KernSmooth_2.23-4    lattice_0.19-13     
[13] latticeExtra_0.6-14  limma_3.6.9          marray_1.28.0       
[16] RColorBrewer_1.0-2   RSQLite_0.9-4        simpleaffy_2.26.1   
[19] splines_2.12.1       stats4_2.12.1        survival_2.36-2     
[22] SVGAnnotation_0.7-2  tools_2.12.1         XML_3.2-0           
[25] xtable_1.5-6