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}}

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

On Tue, Mar 20, 2012 at 10:32 PM, Rosalind Cutts <r.j.cutts@qmul.ac.uk>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 > > I am also getting the same error. > 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@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Thanks very much for the reply, I have tried this with a clean R and bioconductor installation and get a similar error. ArrayQualityMetrics works ok, it just fails to produce some of the graphical output. Cairo version: pkg-config --modversion cairo 1.2.4 When I tried updating Cairo on the Redhat linux machine I am using as suggested by your link there were no updates to load. Is there anything else that you could suggest I could try. Thanks again for your help Ros 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}}