Hi Eric and Wolfgang I haven't been following the low-level details of this, but if either of you can send me the XML document and the stack trace of where the error occurs, I hope that we can tweak the SVGAnnotation code to handle this particular nuance of the SVG this version of cairo generates. D. On 10/9/11 1:15 PM, Paniagua, Eric wrote: > Dear Wolfgang, > > Thank you for another quick and helpful response. As you can see, I definitely have outdated versions of cairo and libxml-2.0: > > $ pkg-config --modversion cairo libxml-2.0 > 1.2.4 > 2.6.26 > > These are the versions for the production environment, which is on a shared server so I will still have to see whether upgrading will be an issue, but it should be less so for upgrades to stable versions. Thanks again for your feedback! > > Best, > Eric > ________________________________________ > From: Wolfgang Huber [whuber at embl.de] > Sent: Sunday, October 09, 2011 2:11 PM > To: Paniagua, Eric > Cc: bioconductor at r-project.org > Subject: Re: [BioC] arrayQualityMetrics NULL XML-node Error; Anyone still getting this? > > Dear Eric > > thank you. I understand your general concern about stability in a > production environment, but specifically here this is not a real problem: > > - Browser: older, released versions of Firefox (e.g. 7.0.1) or Chrome > (and probably others that are HTML5-capable, I have not tried) will be > just as OK. > > - R and Bioconductor: you will then have to wait until the next release, > at the end of this month / early November. > > - cairo and libxml2, actually the version numbers that we exchanged > previously were irrelevant. What is needed it the output of > > $ pkg-config --modversion cairo libxml-2.0 > 1.10.2 > 2.7.8 > > What do you get here? > > cairo version 1.10.2 and libxml-2.0 version 2.7.8 were both released in > 2010, almost a year ago, see http://cairographics.org and > http://xmlsoft.org/news.html > > Best wishes > Wolfgang > > > > Oct/9/11 5:31 AM, Paniagua, Eric scripsit:: >> Dear Wolfgang, >> >> Thanks for taking a look and for your quick response. I will look at the potential upgrades you are suggesting, but I see that several key versions you are using are unstable or development versions including R, your browser, and AQM itself. >> >> I need to produce software for a production system rather than personal use, so I hesitate to introduce dev/unstable dependencies. Do you know offhand the most recent combination of stable versions that work together correctly, for instance with Bioconductor release 2.8? >> >> Thanks, >> Eric >> ________________________________________ >> From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] on behalf of Wolfgang Huber [whuber at embl.de] >> Sent: Saturday, October 08, 2011 9:44 AM >> To: bioconductor at r-project.org >> Subject: Re: [BioC] arrayQualityMetrics NULL XML-node Error; Anyone still getting this? >> >> Dear Eric >> >> thank you for sending a reproducible example. I have run the same code >> as you, and this produced a report without error messages and with all >> elements that are supposed to be interactive (Figs. 3, 6, 12 and the >> table) behaving as expected. The code and the report are here: >> http://www-huber.embl.de/users/whuber/bioc-list/111008/ >> >> I have the following system parameters and session info as below, so my >> recommendation is for you to update to more recent versions. More >> comments see below. >> >> $ pkg-config --version cairo >> 0.26 >> $ xml2-config --version >> 2.7.8 >> # arrayQualityMetrics version: 3.9.5. >> # Firefox 8.0 >> >> > sessionInfo() >> R Under development (unstable) (2011-10-07 r57184) >> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] hgu133acdf_2.8.0 ALLMLL_1.2.8 >> [3] affy_1.31.6 Biobase_2.13.10 >> [5] arrayQualityMetrics_3.9.5 fortunes_1.4-2 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.15.29 BiocInstaller_1.1.28 Biostrings_2.21.11 >> [4] Cairo_1.5-0 DBI_0.2-5 Hmisc_3.8-3 >> [7] IRanges_1.11.27 KernSmooth_2.23-6 RColorBrewer_1.0-5 >> [10] RSQLite_0.10.0 SVGAnnotation_0.9-0 XML_3.4-3 >> [13] affyPLM_1.29.3 affyio_1.21.2 annotate_1.31.1 >> [16] beadarray_2.3.10 cluster_1.14.0 genefilter_1.35.0 >> [19] grid_2.15.0 hwriter_1.3 lattice_0.19-33 >> [22] latticeExtra_0.6-18 limma_3.9.21 preprocessCore_1.15.0 >> [25] reshape_0.8.4 setRNG_2009.11-1 splines_2.15.0 >> [28] survival_2.36-10 tools_2.15.0 vsn_3.21.2 >> [31] xtable_1.5-6 zlibbioc_0.1.8 >> >> ------------------------------------------------ >> The fact that for you Figs. 6 and 12 'work' -these are line plots- and >> that Fig. 3 does not -this is a scatter plot- suggests that what you are >> encountering is an aspect of the brittleness in the way that >> arrayQualityMetrics (via SVGAnnotation) interacts with SVG files >> produced by a third party (cairo). Essentially, that interaction is not >> based on a defined protocol, but on unilateral reverse engineering. >> >> SVGAnnotation is a fantastic piece of 'proof of concept' software, but >> the situation is, of course, not satisfatory for applications that are >> supposed to be used by many different people and on different platforms. >> As soon as I can find the time, I will see how it can improved ( e.g. >> gridSVG, where we have more control over the SVG ). >> >> Best wishes >> Wolfgang >> >> >> Oct/7/11 8:59 PM, Paniagua, Eric scripsit:: >>> Hi Bioconductors (hopefully still including Wolfgang), >>> >>> I have updated my packages, as per this list's posting guide, but to no avail. I have also searched the archives, and I discovered this thread where someone had a very similar problem (http://thread.gmane.o rg/gmane.science.biology.informatics.conductor/31622/focus=31666). I do not see there any solution. It's been about a year since that thread circulated, so I was wondering if anyone else has encountered this XML problem when running arrayQualityMetrics. >>> >>> It is not clear that my error is exactly the same as what James (from the above thread) encountered, but I'm thinking it's likely related. Maybe there is a parallel code block to the one throwing an error for James that wasn't fixed and is only now being observed. The differences from James's report follow: >>> >>> 1) I do get sections 4 and 5 in the index.html report file. >>> >>> 2) I have a notice beneath the caption for Figure 3 which reads: "Note: the figure is static - enhancement with interactive effects failed. This is either due to a version incompatibility of the 'SVGAnnotation' R package and your version of 'Cairo' or 'libcairo', or due to plot misformating. Please consult the Bioconductor mailing list, or contact the maintainer of 'arrayQualityMetrics' with a reproducible example in order to fix this problem." >>> >>> $ pkg-config --version cairo >>> 0.21 >>> >>> $ xml2-config --version >>> 2.6.26 >>> >>> The binary libcairo file installed is at /usr/lib64/libcairo.so.2.9.2 >>> >>> Figures 6 and 12 *are* interactive, which leads me to think it could be either a version mismatch issue between libcairo and SVGAnnotation or a code issue in the arrayQualityMetrics package itself. >>> >>> I also have another case with the same error manifesting slightly differently, but I figure it's best to have everything working correctly for sample code from the vignette first (http://www.biocondu ctor.org/packages/2.8/bioc/vignettes/arrayQualityMetrics/inst/doc/arra yQualityMetrics.pdf and below). I notice that some of my versions are slightly newer than those from the vignette. >>> >>> Details: >>> * R was run as: R --vanilla >>> * R and all packages are installed on a 48-core server, 64-bit, running CentOS 5.5 (final) >>> * For viewing, I copied the output to my local machine (dual-core laptop running Ubuntu 10.10) >>> * I viewed index.html in Google Chrome 14.0.835.186 >>> >>> My example R session demonstrating the error follows. >>> >>> I would greatly appreciate any feedback, suggestions, questions, and/or answers you may be able to provide. >>> >>> Thanks, >>> Eric Paniagua >>> >>> PS: I apologize for the lack of monospace font in what follows; I can't find how to set it in the OWA client. >>> >>> R version 2.13.1 (2011-07-08) >>> Copyright (C) 2011 The R Foundation for Statistical Computing >>> ISBN 3-900051-07-0 >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>> You are welcome to redistribute it under certain conditions. >>> Type 'license()' or 'licence()' for distribution details. >>> >>> R is a collaborative project with many contributors. >>> Type 'contributors()' for more information and >>> 'citation()' on how to cite R or R packages in publications. >>> >>> Type 'demo()' for some demos, 'help()' for on-line help, or >>> 'help.start()' for an HTML browser interface to help. >>> Type 'q()' to quit R. >>> >>>> library("ALLMLL") >>> Loading required package: affy >>> Loading required package: Biobase >>> >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material. To view, type >>> 'browseVignettes()'. To cite Bioconductor, see >>> 'citation("Biobase")' and for packages 'citation("pkgname")'. >>> >>>> data("MLL.A") >>>> library("arrayQualityMetrics") >>>> arrayQualityMetrics(expressionset = MLL.A[, 1:5], >>> + outdir = "Report_for_MLL_A", >>> + force = TRUE, >>> + do.logtransform = TRUE) >>> The directory 'Report_for_MLL_A' has been created. >>> Error in UseMethod("xmlAttrs", node) : >>> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>> KernSmooth 2.23 loaded >>> Copyright M. P. Wand 1997-2009 >>>> traceback() >>> No traceback available >>>> warnings() >>> NULL >>>> sessionInfo() >>> R version 2.13.1 (2011-07-08) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] hgu133acdf_2.8.0 arrayQualityMetrics_3.8.0 >>> [3] ALLMLL_1.2.8 affy_1.30.0 >>> [5] Biobase_2.12.2 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.14.1 Biostrings_2.20.4 Cairo_1.5-0 >>> [4] DBI_0.2-5 Hmisc_3.8-3 IRanges_1.10.6 >>> [7] KernSmooth_2.23-6 RColorBrewer_1.0-5 RSQLite_0.10.0 >>> [10] SVGAnnotation_0.9-0 XML_3.4-3 affyPLM_1.28.5 >>> [13] affyio_1.20.0 annotate_1.30.1 beadarray_2.2.0 >>> [16] cluster_1.14.0 genefilter_1.34.0 grid_2.13.1 >>> [19] hwriter_1.3 lattice_0.19-33 latticeExtra_0.6-18 >>> [22] limma_3.8.3 preprocessCore_1.14.0 setRNG_2009.11-1 >>> [25] splines_2.13.1 survival_2.36-10 tools_2.13.1 >>> [28] vsn_3.20.0 xtable_1.5-6 >>> _______________________________________________ >>> 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 >> >> >> -- >> >> >> 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 > > > -- > > > 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

Dear Eric yes - cairo 1.2 is way out of date, and I am pretty sure that that is the culprit (it was before, in similar cases). You'll need to ask your server admin to update that. The cost of using bleeing-edge tools... :) Best wishes Wolfgang Oct/9/11 10:15 PM, Paniagua, Eric scripsit:: > Dear Wolfgang, > > Thank you for another quick and helpful response. As you can see, I definitely have outdated versions of cairo and libxml-2.0: > > $ pkg-config --modversion cairo libxml-2.0 > 1.2.4 > 2.6.26 > > These are the versions for the production environment, which is on a shared server so I will still have to see whether upgrading will be an issue, but it should be less so for upgrades to stable versions. Thanks again for your feedback! > > Best, > Eric > ________________________________________ > From: Wolfgang Huber [whuber at embl.de] > Sent: Sunday, October 09, 2011 2:11 PM > To: Paniagua, Eric > Cc: bioconductor at r-project.org > Subject: Re: [BioC] arrayQualityMetrics NULL XML-node Error; Anyone still getting this? > > Dear Eric > > thank you. I understand your general concern about stability in a > production environment, but specifically here this is not a real problem: > > - Browser: older, released versions of Firefox (e.g. 7.0.1) or Chrome > (and probably others that are HTML5-capable, I have not tried) will be > just as OK. > > - R and Bioconductor: you will then have to wait until the next release, > at the end of this month / early November. > > - cairo and libxml2, actually the version numbers that we exchanged > previously were irrelevant. What is needed it the output of > > $ pkg-config --modversion cairo libxml-2.0 > 1.10.2 > 2.7.8 > > What do you get here? > > cairo version 1.10.2 and libxml-2.0 version 2.7.8 were both released in > 2010, almost a year ago, see http://cairographics.org and > http://xmlsoft.org/news.html > > Best wishes > Wolfgang > > > > Oct/9/11 5:31 AM, Paniagua, Eric scripsit:: >> Dear Wolfgang, >> >> Thanks for taking a look and for your quick response. I will look at the potential upgrades you are suggesting, but I see that several key versions you are using are unstable or development versions including R, your browser, and AQM itself. >> >> I need to produce software for a production system rather than personal use, so I hesitate to introduce dev/unstable dependencies. Do you know offhand the most recent combination of stable versions that work together correctly, for instance with Bioconductor release 2.8? >> >> Thanks, >> Eric >> ________________________________________ >> From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] on behalf of Wolfgang Huber [whuber at embl.de] >> Sent: Saturday, October 08, 2011 9:44 AM >> To: bioconductor at r-project.org >> Subject: Re: [BioC] arrayQualityMetrics NULL XML-node Error; Anyone still getting this? >> >> Dear Eric >> >> thank you for sending a reproducible example. I have run the same code >> as you, and this produced a report without error messages and with all >> elements that are supposed to be interactive (Figs. 3, 6, 12 and the >> table) behaving as expected. The code and the report are here: >> http://www-huber.embl.de/users/whuber/bioc-list/111008/ >> >> I have the following system parameters and session info as below, so my >> recommendation is for you to update to more recent versions. More >> comments see below. >> >> $ pkg-config --version cairo >> 0.26 >> $ xml2-config --version >> 2.7.8 >> # arrayQualityMetrics version: 3.9.5. >> # Firefox 8.0 >> >> > sessionInfo() >> R Under development (unstable) (2011-10-07 r57184) >> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] hgu133acdf_2.8.0 ALLMLL_1.2.8 >> [3] affy_1.31.6 Biobase_2.13.10 >> [5] arrayQualityMetrics_3.9.5 fortunes_1.4-2 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.15.29 BiocInstaller_1.1.28 Biostrings_2.21.11 >> [4] Cairo_1.5-0 DBI_0.2-5 Hmisc_3.8-3 >> [7] IRanges_1.11.27 KernSmooth_2.23-6 RColorBrewer_1.0-5 >> [10] RSQLite_0.10.0 SVGAnnotation_0.9-0 XML_3.4-3 >> [13] affyPLM_1.29.3 affyio_1.21.2 annotate_1.31.1 >> [16] beadarray_2.3.10 cluster_1.14.0 genefilter_1.35.0 >> [19] grid_2.15.0 hwriter_1.3 lattice_0.19-33 >> [22] latticeExtra_0.6-18 limma_3.9.21 preprocessCore_1.15.0 >> [25] reshape_0.8.4 setRNG_2009.11-1 splines_2.15.0 >> [28] survival_2.36-10 tools_2.15.0 vsn_3.21.2 >> [31] xtable_1.5-6 zlibbioc_0.1.8 >> >> ------------------------------------------------ >> The fact that for you Figs. 6 and 12 'work' -these are line plots- and >> that Fig. 3 does not -this is a scatter plot- suggests that what you are >> encountering is an aspect of the brittleness in the way that >> arrayQualityMetrics (via SVGAnnotation) interacts with SVG files >> produced by a third party (cairo). Essentially, that interaction is not >> based on a defined protocol, but on unilateral reverse engineering. >> >> SVGAnnotation is a fantastic piece of 'proof of concept' software, but >> the situation is, of course, not satisfatory for applications that are >> supposed to be used by many different people and on different platforms. >> As soon as I can find the time, I will see how it can improved ( e.g. >> gridSVG, where we have more control over the SVG ). >> >> Best wishes >> Wolfgang >> >> >> Oct/7/11 8:59 PM, Paniagua, Eric scripsit:: >>> Hi Bioconductors (hopefully still including Wolfgang), >>> >>> I have updated my packages, as per this list's posting guide, but to no avail. I have also searched the archives, and I discovered this thread where someone had a very similar problem (http://thread.gmane.o rg/gmane.science.biology.informatics.conductor/31622/focus=31666). I do not see there any solution. It's been about a year since that thread circulated, so I was wondering if anyone else has encountered this XML problem when running arrayQualityMetrics. >>> >>> It is not clear that my error is exactly the same as what James (from the above thread) encountered, but I'm thinking it's likely related. Maybe there is a parallel code block to the one throwing an error for James that wasn't fixed and is only now being observed. The differences from James's report follow: >>> >>> 1) I do get sections 4 and 5 in the index.html report file. >>> >>> 2) I have a notice beneath the caption for Figure 3 which reads: "Note: the figure is static - enhancement with interactive effects failed. This is either due to a version incompatibility of the 'SVGAnnotation' R package and your version of 'Cairo' or 'libcairo', or due to plot misformating. Please consult the Bioconductor mailing list, or contact the maintainer of 'arrayQualityMetrics' with a reproducible example in order to fix this problem." >>> >>> $ pkg-config --version cairo >>> 0.21 >>> >>> $ xml2-config --version >>> 2.6.26 >>> >>> The binary libcairo file installed is at /usr/lib64/libcairo.so.2.9.2 >>> >>> Figures 6 and 12 *are* interactive, which leads me to think it could be either a version mismatch issue between libcairo and SVGAnnotation or a code issue in the arrayQualityMetrics package itself. >>> >>> I also have another case with the same error manifesting slightly differently, but I figure it's best to have everything working correctly for sample code from the vignette first (http://www.biocondu ctor.org/packages/2.8/bioc/vignettes/arrayQualityMetrics/inst/doc/arra yQualityMetrics.pdf and below). I notice that some of my versions are slightly newer than those from the vignette. >>> >>> Details: >>> * R was run as: R --vanilla >>> * R and all packages are installed on a 48-core server, 64-bit, running CentOS 5.5 (final) >>> * For viewing, I copied the output to my local machine (dual-core laptop running Ubuntu 10.10) >>> * I viewed index.html in Google Chrome 14.0.835.186 >>> >>> My example R session demonstrating the error follows. >>> >>> I would greatly appreciate any feedback, suggestions, questions, and/or answers you may be able to provide. >>> >>> Thanks, >>> Eric Paniagua >>> >>> PS: I apologize for the lack of monospace font in what follows; I can't find how to set it in the OWA client. >>> >>> R version 2.13.1 (2011-07-08) >>> Copyright (C) 2011 The R Foundation for Statistical Computing >>> ISBN 3-900051-07-0 >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>> You are welcome to redistribute it under certain conditions. >>> Type 'license()' or 'licence()' for distribution details. >>> >>> R is a collaborative project with many contributors. >>> Type 'contributors()' for more information and >>> 'citation()' on how to cite R or R packages in publications. >>> >>> Type 'demo()' for some demos, 'help()' for on-line help, or >>> 'help.start()' for an HTML browser interface to help. >>> Type 'q()' to quit R. >>> >>>> library("ALLMLL") >>> Loading required package: affy >>> Loading required package: Biobase >>> >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material. To view, type >>> 'browseVignettes()'. To cite Bioconductor, see >>> 'citation("Biobase")' and for packages 'citation("pkgname")'. >>> >>>> data("MLL.A") >>>> library("arrayQualityMetrics") >>>> arrayQualityMetrics(expressionset = MLL.A[, 1:5], >>> + outdir = "Report_for_MLL_A", >>> + force = TRUE, >>> + do.logtransform = TRUE) >>> The directory 'Report_for_MLL_A' has been created. >>> Error in UseMethod("xmlAttrs", node) : >>> no applicable method for 'xmlAttrs' applied to an object of class "NULL" >>> KernSmooth 2.23 loaded >>> Copyright M. P. Wand 1997-2009 >>>> traceback() >>> No traceback available >>>> warnings() >>> NULL >>>> sessionInfo() >>> R version 2.13.1 (2011-07-08) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] hgu133acdf_2.8.0 arrayQualityMetrics_3.8.0 >>> [3] ALLMLL_1.2.8 affy_1.30.0 >>> [5] Biobase_2.12.2 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.14.1 Biostrings_2.20.4 Cairo_1.5-0 >>> [4] DBI_0.2-5 Hmisc_3.8-3 IRanges_1.10.6 >>> [7] KernSmooth_2.23-6 RColorBrewer_1.0-5 RSQLite_0.10.0 >>> [10] SVGAnnotation_0.9-0 XML_3.4-3 affyPLM_1.28.5 >>> [13] affyio_1.20.0 annotate_1.30.1 beadarray_2.2.0 >>> [16] cluster_1.14.0 genefilter_1.34.0 grid_2.13.1 >>> [19] hwriter_1.3 lattice_0.19-33 latticeExtra_0.6-18 >>> [22] limma_3.8.3 preprocessCore_1.14.0 setRNG_2009.11-1 >>> [25] splines_2.13.1 survival_2.36-10 tools_2.13.1 >>> [28] vsn_3.20.0 xtable_1.5-6 >>> _______________________________________________ >>> 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 >> >> >> -- >> >> >> 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 > > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber