[BioC] Problems using arrayQualityMetrics

[Wolfgang Huber]

Dear Ros and Reema

thanks for using up-to-date versions of R & Bioconductor. I am surprised 
by what you give as the output of 'traceback', I have never seen that. 
Does it mean that you cannot even load the package 'arrayQualityMetrics'?

I have two suggestions:

- Make sure that you are working with a clean R installation; try on a 
different computer and see if the problem reproduces.

- There is one more component on your system which may need updating. 
What do you get from:
   pkg-config --modversion cairo

arrayQualityMetrics uses SVGAnnotation which in turn relies on a system 
library (i.e. not an R package) on your computer called 'cairo'. I have 
tested arrayQualityMetrics with version 1.10.2. If what you have is an 
older version, and you get error messages or warnings, then please 
update that system library. (How to do so depends on your operating 
system, see http://cairographics.org/download )

	Best wishes, let me know how it goes
	Wolfgang

On 3/20/12 6:02 PM, Rosalind Cutts wrote:
> Hi
>
> I’m trying to use the arrayQualityMetrics package and get the following error:
>
> Error in UseMethod("xmlAttrs", node) :
>    no applicable method for 'xmlAttrs' applied to an object of class "NULL"
> KernSmooth 2.23 loaded
>
> Having seen some posts similar to this from about a year or so ago I have tried updating R and bioconductor but still get the same error.
>
> Basically the first set of graphs are created and then the error occurs.
>
> See additonal information below.
>
> Would you have some suggestions of what to try next.
>
> Thanks
> Ros Cutts
> Barts Cancer Institute
>
> traceback()
> 2: stop(txt, domain = NA)
> 1: library("arrayQualityMetrics")
>
>
>> sessionInfo()
> R version 2.14.2 (2012-02-29)
> 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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 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_2.9.1       AnnotationDbi_1.16.19
> [3] limma_3.10.3               affy_1.32.1
> [5] Biobase_2.14.0             arrayQualityMetrics_3.10.0
> [7] BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.22.0         affyPLM_1.30.0        annotate_1.32.3
>   [4] beadarray_2.4.2       Biostrings_2.22.0     Cairo_1.5-1
>   [7] cluster_1.14.2        colorspace_1.1-1      DBI_0.2-5
> [10] genefilter_1.36.0     grid_2.14.2           Hmisc_3.9-2
> [13] hwriter_1.3           IRanges_1.12.6        KernSmooth_2.23-7
> [16] lattice_0.20-6        latticeExtra_0.6-19   plyr_1.7.1
> [19] preprocessCore_1.16.0 RColorBrewer_1.0-5    reshape2_1.2.1
> [22] RSQLite_0.11.1        setRNG_2009.11-1      splines_2.14.2
> [25] stringr_0.6           survival_2.36-12      SVGAnnotation_0.9-0
> [28] tools_2.14.2          vsn_3.22.0            XML_3.9-4
> [31] xtable_1.7-0          zlibbioc_1.0.1
>
>
>
>
>
>
>
>
>
>
> This email may contain information that is privileged, confidential or otherwise protected from disclosure.
> It must not be used by, or its contents copied or disclosed to, persons other than the addressee.
> If you have received this email in error please notify the sender immediately and delete the email.
> This message has been scanned for viruses.\ \ \ 	[[alter...{{dropped:6}}
>
>
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber