[BioC] arrayQualityMetrics NULL XML-node Error; Anyone still getting this?
Duncan Temple Lang
duncan at wald.ucdavis.edu
Sun Oct 9 22:19:55 CEST 2011
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 As you can see, I definitely have outdated versions of cairo and libxml-2.0: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.org/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.bioconductor.org/packages/2.8/bioc/vignettes/arrayQualityMetrics/inst/doc/arrayQualityMetrics.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
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