[BioC] R: arrayQualityMetrics error

Wed Feb 9 22:44:39 CET 2011

Hi 

Here it is:

Error in UseMethod("xmlAttrs", node) : 
  no applicable method for 'xmlAttrs' applied to an object of class "NULL"
In addition: There were 38 warnings (use warnings() to see them)
> traceback()
18: xmlAttrs(node, addNamespace)
17: xmlGetAttr(clipPath[["path"]], "d")
16: getRect(xmlGetAttr(clipPath[["path"]], "d"))
15: getPlotRegion(n)
14: FUN(X[[1L]], ...)
13: lapply(X, FUN, ...)
12: sapply(tmp, function(n) all(getPlotRegion(n) == vb))
11: getPlotRegionNodes(doc)
10: is.vector(X)
9: lapply(getPlotRegionNodes(doc), getPlotPoints)
8: getPlotPoints.XMLInternalDocument(doc)
7: annotationInfo$getfun(doc)
6: aqm.highlight(doc, annotationInfo = annotationInfo)
5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg)
4: aqm.report.qm(p, obj[[i]], i, names(obj)[i])
3: aqm.writereport(reporttitle, expressionset, obj)
2: arrayQualityMetrics(rawAffyData, outdir = "output/quality", force = T)
1: arrayQualityMetrics(rawAffyData, outdir = "output/quality", force = T)
> 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 

BTW, I'm running on CentOS release 5.5 (Final) and libxml2 is

libxml2-2.6.26-2.1.2.8.el5_5.1

Thanks

Paulo

On 2011-02-09, at 4:02 PM, Manca Marco (PATH) wrote:

> 
> Could it be related to the installation of the library libxml2 on your linux machine?
> 
> Could you give us your capabilities() and traceback() after the error message?
> 
> All the best, Marco
> 
> --
> Marco Manca, MD
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
> 
> Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
> Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08,  Maastricht University Medical Center, P. Debyelaan 25, 6229  HX Maastricht
> 
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> Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] per conto di Paulo Nuin [nuin at genedrift.org]
> Inviato: mercoledì 9 febbraio 2011 21.38
> A: bioconductor at stat.math.ethz.ch
> Oggetto: [BioC] arrayQualityMetrics error
> 
> 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
> 
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