[BioC] arrayQualityMetrics error

[Paulo Nuin]

Hi James

I checked our Cairo version, and it seems quite old. I'm checking the best way to update, as we are using CentOS official package. If the problem persists after upgrade, I will report to the list.

Thanks a lot for your help.

Paulo


On 2011-02-09, at 4:03 PM, James F. Reid wrote:

> 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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