Problems using arrayQualityMetrics
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@rosalind-cutts-5179
Last seen 7.1 years ago
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}}
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@wolfgang-huber-3550
Last seen 1 day ago
EMBL European Molecular Biology Laborat…
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Reema Singh ▴ 570
@reema-singh-4373
Last seen 7.1 years ago
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]]
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@rosalind-cutts-5179
Last seen 7.1 years ago
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}}
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Dear Wolfgang, Ros's computer definitely needs an upgrade. However, looking breifly into this, here is the offending line of code from arrayQualityMetrics::aqm.report.qm(...) size = annotateSvgMatplot(svgtemp, nameimg, annotationInfo=qm$svg) The above fails while generating pca.svg and rnadeg.svg. Interestingly density.svg comes out *okish*. The density plot looks correct but without axis-labels and legends. All other figures are fine too, including the pdf equivalent of all svgs. Best, Syed On 22/03/2012 23:39, Wolfgang Huber wrote: > Dear Rosalind > > unfortunately, the fact that the package manager on your Redhat Linux > does not provide you with a newer version does not mean that there is > none. The Linux distribution that you are using seems to be very much > behind in time: cairo 1.2.4 is from 2006, see http://cairographics.org/ > > Two options: > - use a system that is better kept up-to-date > - remove the cairo that your package manager gives you, and install > libcairo >=1.10.2 'manually' by downloading it from the above URL. > > Btw, I would also also prefer if arrayQualityMetrics (i.e., really the > SVGAnnotation package) was backwards compatible with any old version of > cairo, but that is not a realistic expectation (neither for our > software, nor for many other products, incl. commercial). > > Best wishes > Wolfgang > > Mar/22/12 12:38 PM, Rosalind Cutts scripsit:: >> 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 > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > 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 ADD REPLY 0 Entering edit mode Dear Syed thanks! With what version of 'arrayQualityMetrics' did you experience this? As far as I can tell, the function 'annotateSvgMatplot' was last used in Bioconductor release 2.7 from autumn 2010. To use this package, please, please use a *current version of R, Bioconductor, and the cairo graphics* library. Please do not expect that any old combination of these components will work together. Also, you would be missing out on the cool new features. I recommend using http://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMetri cs.html, which is close to release. PS - OKish looking plots are one thing, but SVGAnnotation postprocesses the SVG code for the plots and requires that that code is quite precisely as expected. Enjoy, Wolfgang Mar/23/12 1:04 AM, Syed Haider scripsit:: > Dear Wolfgang, > > Ros's computer definitely needs an upgrade. However, looking breifly > into this, here is the offending line of code from > arrayQualityMetrics::aqm.report.qm(...) > > size = annotateSvgMatplot(svgtemp, nameimg, annotationInfo=qm$svg) > > The above fails while generating pca.svg and rnadeg.svg. Interestingly > density.svg comes out *okish*. The density plot looks correct but > without axis-labels and legends. All other figures are fine too, > including the pdf equivalent of all svgs. > > > Best, > Syed > > > On 22/03/2012 23:39, Wolfgang Huber wrote: >> Dear Rosalind >> >> unfortunately, the fact that the package manager on your Redhat Linux >> does not provide you with a newer version does not mean that there is >> none. The Linux distribution that you are using seems to be very much >> behind in time: cairo 1.2.4 is from 2006, see http://cairographics.org/ >> >> Two options: >> - use a system that is better kept up-to-date >> - remove the cairo that your package manager gives you, and install >> libcairo >=1.10.2 'manually' by downloading it from the above URL. >> >> Btw, I would also also prefer if arrayQualityMetrics (i.e., really the >> SVGAnnotation package) was backwards compatible with any old version of >> cairo, but that is not a realistic expectation (neither for our >> software, nor for many other products, incl. commercial). >> >> Best wishes >> Wolfgang >> >> Mar/22/12 12:38 PM, Rosalind Cutts scripsit:: >>> 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 >> >> >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> _______________________________________________ >> 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
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Thanks Wolfgang for your detailed reply. The machine which i tried this on had: arrayQualityMetrics v3.2.4 (installed from source) R v2.12.2 System wide Cairo v1.2.4 R Cairo v1.5-1 I guess Ros et al have tried this on the latest versions too. Thanks, Syed On 23/03/2012 08:12, Wolfgang Huber wrote: > Dear Syed > > thanks! With what version of 'arrayQualityMetrics' did you experience > this? As far as I can tell, the function 'annotateSvgMatplot' was last > used in Bioconductor release 2.7 from autumn 2010. > > To use this package, please, please use a *current version of R, > Bioconductor, and the cairo graphics* library. > > Please do not expect that any old combination of these components will > work together. Also, you would be missing out on the cool new features. > > I recommend using > http://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMet rics.html, > which is close to release. > > PS - OKish looking plots are one thing, but SVGAnnotation postprocesses > the SVG code for the plots and requires that that code is quite > precisely as expected. > > Enjoy, > Wolfgang > > Mar/23/12 1:04 AM, Syed Haider scripsit:: >> Dear Wolfgang, >> >> Ros's computer definitely needs an upgrade. However, looking breifly >> into this, here is the offending line of code from >> arrayQualityMetrics::aqm.report.qm(...) >> >> size = annotateSvgMatplot(svgtemp, nameimg, annotationInfo=qm$svg) >> >> The above fails while generating pca.svg and rnadeg.svg. Interestingly >> density.svg comes out *okish*. The density plot looks correct but >> without axis-labels and legends. All other figures are fine too, >> including the pdf equivalent of all svgs. >> >> >> Best, >> Syed >> >> >> On 22/03/2012 23:39, Wolfgang Huber wrote: >>> Dear Rosalind >>> >>> unfortunately, the fact that the package manager on your Redhat Linux >>> does not provide you with a newer version does not mean that there is >>> none. The Linux distribution that you are using seems to be very much >>> behind in time: cairo 1.2.4 is from 2006, see http://cairographics.org/ >>> >>> Two options: >>> - use a system that is better kept up-to-date >>> - remove the cairo that your package manager gives you, and install >>> libcairo >=1.10.2 'manually' by downloading it from the above URL. >>> >>> Btw, I would also also prefer if arrayQualityMetrics (i.e., really the >>> SVGAnnotation package) was backwards compatible with any old version of >>> cairo, but that is not a realistic expectation (neither for our >>> software, nor for many other products, incl. commercial). >>> >>> Best wishes >>> Wolfgang >>> >>> Mar/22/12 12:38 PM, Rosalind Cutts scripsit:: >>>> 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 >>> >>> >>> Wolfgang Huber >>> EMBL >>> http://www.embl.de/research/units/genome_biology/huber >>> >>> _______________________________________________ >>> 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 > > ADD REPLY 0 Entering edit mode Dear Syed Mar/23/12 11:57 AM, Syed Haider scripsit:: > Thanks Wolfgang for your detailed reply. > The machine which i tried this on had: > > arrayQualityMetrics v3.2.4 (installed from source) > R v2.12.2 > System wide Cairo v1.2.4 > R Cairo v1.5-1 All of these are old and outdated. > I guess Ros et al have tried this on the latest versions too. Ros used a recent R and Bioconductor, but still a much too old cairo graphics library. Best wishes Wolfgang > > Thanks, > Syed > > > > On 23/03/2012 08:12, Wolfgang Huber wrote: >> Dear Syed >> >> thanks! With what version of 'arrayQualityMetrics' did you experience >> this? As far as I can tell, the function 'annotateSvgMatplot' was last >> used in Bioconductor release 2.7 from autumn 2010. >> >> To use this package, please, please use a *current version of R, >> Bioconductor, and the cairo graphics* library. >> >> Please do not expect that any old combination of these components will >> work together. Also, you would be missing out on the cool new features. >> >> I recommend using >> http://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMe trics.html, >> >> which is close to release. >> >> PS - OKish looking plots are one thing, but SVGAnnotation postprocesses >> the SVG code for the plots and requires that that code is quite >> precisely as expected. >> >> Enjoy, >> Wolfgang >> >> Mar/23/12 1:04 AM, Syed Haider scripsit:: >>> Dear Wolfgang, >>> >>> Ros's computer definitely needs an upgrade. However, looking breifly >>> into this, here is the offending line of code from >>> arrayQualityMetrics::aqm.report.qm(...) >>> >>> size = annotateSvgMatplot(svgtemp, nameimg, annotationInfo=qm$svg) >>> >>> The above fails while generating pca.svg and rnadeg.svg. Interestingly >>> density.svg comes out *okish*. The density plot looks correct but >>> without axis-labels and legends. All other figures are fine too, >>> including the pdf equivalent of all svgs. >>> >>> >>> Best, >>> Syed >>> >>> >>> On 22/03/2012 23:39, Wolfgang Huber wrote: >>>> Dear Rosalind >>>> >>>> unfortunately, the fact that the package manager on your Redhat Linux >>>> does not provide you with a newer version does not mean that there is >>>> none. The Linux distribution that you are using seems to be very much >>>> behind in time: cairo 1.2.4 is from 2006, see http://cairographics.org/ >>>> >>>> Two options: >>>> - use a system that is better kept up-to-date >>>> - remove the cairo that your package manager gives you, and install >>>> libcairo >=1.10.2 'manually' by downloading it from the above URL. >>>> >>>> Btw, I would also also prefer if arrayQualityMetrics (i.e., really the >>>> SVGAnnotation package) was backwards compatible with any old version of >>>> cairo, but that is not a realistic expectation (neither for our >>>> software, nor for many other products, incl. commercial). >>>> >>>> Best wishes >>>> Wolfgang >>>> >>>> Mar/22/12 12:38 PM, Rosalind Cutts scripsit:: >>>>> 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 >>>> >>>> >>>> Wolfgang Huber >>>> EMBL >>>> http://www.embl.de/research/units/genome_biology/huber >>>> >>>> _______________________________________________ >>>> 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