[BioC] arrayQualityMetrics error

[James F. Reid]

Hi Paulo,


On 02/09/2011 09:38 PM, Paulo Nuin wrote:
> 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)

The same happened on my system, the problem was a very old version of 
cairo, see this thread:
https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html
Either upgrade if you can or try using the devel version which I believe 
detects the capabilites of the system before running and producing 
annotated svg figures or not.

HTH,
James.



>
> 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
>
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