[BioC] arrayQualityMetrics error
Paulo Nuin
nuin at genedrift.org
Fri Feb 11 13:26:28 CET 2011
Hi Wolfgang
Indeed, if I create an X11 tunnel, everything turns ok on the X11 side. My mistake, as the system is remote and some of the tests we run on a local machine.
Nonetheless, we still find a problem at the end of the run, and it's similar to what we experienced the first time. Here is the error and traceback:
> arrayQualityMetrics(rawAffyData, outdir="quality", force=T)
The report will be written into directory 'quality'.
Error in UseMethod("xmlAttrs", node) :
no applicable method for 'xmlAttrs' applied to an object of class "NULL"
> traceback()
16: xmlAttrs(node, addNamespace)
15: xmlGetAttr(clipPath[["path"]], "d")
14: getRect(xmlGetAttr(clipPath[["path"]], "d"))
13: getPlotRegion(n)
12: FUN(X[[1L]], ...)
11: lapply(X, FUN, ...)
10: sapply(tmp, function(n) all(getPlotRegion(n) == vb))
9: getPlotRegionNodes(doc)
8: is.vector(X)
7: lapply(getPlotRegionNodes(doc), getPlotPoints)
6: getPlotPoints.XMLInternalDocument(doc)
5: annotationInfo at getPlotObjNodes(doc)
4: annotateSvgPlot(infile = svgtemp, outfile = nameimg, outdir = outdir,
annotationInfo = module at svg, name = name)
3: reportModule(p = p, module = modules[[i]], currentIndex = currentIndex,
arrayTable = arrayTableCompact, outdir = outdir)
2: aqm.writereport(modules = m, arrayTable = x$pData, reporttitle = reporttitle,
outdir = outdir)
1: arrayQualityMetrics(rawAffyData, outdir = "quality", force = T)
I guess this is still related to Cairo's version. I will probably try to use another version of Linux in another machine.
Thanks again. If I have any comments or ideas for the package, I let you know.
Cheers
Paulo
On 2011-02-10, at 3:19 PM, Wolfgang Huber wrote:
> Paulo
>
> what happens if you type
>
> system("xclock&")
>
> (Or, in the Unix shell, simply "xclock&"). Do you see a clock?
>
> One possible explanation, if you are logging into a server remotely, that you have not enable X11 forwarding.
>
> Why R's png() device needs an X11 server is a different story...
>
> Best wishes
> Wolfgang
>
> Il Feb/10/11 9:11 PM, Paulo Nuin ha scritto:
>> Hi Wolfgang
>>
>> Thanks a lot for your message. I was able to install this version, both on a release version and on a devel version of R, but I'm running into an error again:
>>
>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T)
>> The report will be written into directory 'quality'.
>> Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, :
>> unable to start device PNG
>> In addition: Warning message:
>> In png(file = nameimg, h = h * dpi, w = w * dpi) :
>> unable to open connection to X11 display ''
>>
>> Here are the capabilities
>>
>>> capabilities()
>> jpeg png tiff tcltk X11 aqua http/ftp sockets
>> TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE
>> libxml fifo cledit iconv NLS profmem cairo
>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE
>>
>>
>> Both versions are the same. I don't know if the error is due to X11 being FALSE. I don't understand why X11 is showing as FALSE, as the binaries were compiled with the --with-x flag, and at the end of configure we got
>>
>> Interfaces supported: X11
>> External libraries: readline
>> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo
>> Options enabled: shared BLAS, R profiling
>>
>> All X11 (xorg-devel) libraries are installed.
>>
>> Thanks again for the help.
>>
>> Cheers
>> Paulo
>>
>>
>>
>>
>> On 2011-02-10, at 1:26 PM, Wolfgang Huber wrote:
>>
>>> Dear Paulo
>>>
>>> there have been many improvements on the package since the last release, and I would recommend trying the devel version>=3.4.8
>>>
>>> http://bioconductor.org/help/bioc-views/2.8/bioc/html/arrayQualityMetrics.html
>>>
>>> which afaIcs will run well on R 2.12. One of the advantages is that it uses Simon Urbanek's "Cairo" package, which brings its own cairo library rather than relying on what it finds on the host system [1] - this should solve your problem.
>>>
>>> The package is in a state of beta-testing, with
>>> - the presentation of the outlier detection in the reports not yet fully cooked,
>>> - and I am not yet sure whether& how well it works on 64bit Windows.
>>>
>>> I hope to finalise this within a week or three; any user experiences and comments are welcome.
>>>
>>> A sneal preview of the new reports is here [2].
>>>
>>> Wolfgang
>>>
>>>
>>> [1] https://stat.ethz.ch/pipermail/bioconductor/attachments/20110128/ca068c82/attachment.pl
>>> [2] http://www-huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN
>>>
>>>
>>> Paulo Nuin scripsit 10/02/11 02:10:
>>>> Hi James
>>>>
>>>> I checked our Cairo version, and it seems quite old. I'm checking the best way to update, as we are using CentOS official package. If the problem persists after upgrade, I will report to the list.
>>>>
>>>> Thanks a lot for your help.
>>>>
>>>> Paulo
>>>>
>>>>
>>>> On 2011-02-09, at 4:03 PM, James F. Reid wrote:
>>>>
>>>>> Hi Paulo,
>>>>>
>>>>>
>>>>> On 02/09/2011 09:38 PM, Paulo Nuin wrote:
>>>>>> Hi everyone
>>>>>>
>>>>>> We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run.
>>>>>>
>>>>>> It goes fine until section 5, were it is interrupted by an error
>>>>>>
>>>>>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T)
>>>>>> The report will be written into directory 'quality'.
>>>>>> [[1]]
>>>>>>
>>>>>> [[2]]
>>>>>>
>>>>>> [[3]]
>>>>>>
>>>>>> [[4]]
>>>>>>
>>>>>> Error in UseMethod("xmlAttrs", node) :
>>>>>> no applicable method for 'xmlAttrs' applied to an object of class "NULL"
>>>>>> In addition: There were 39 warnings (use warnings() to see them)
>>>>>
>>>>> The same happened on my system, the problem was a very old version of cairo, see this thread:
>>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html
>>>>> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not.
>>>>>
>>>>> HTH,
>>>>> James.
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>> Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated.
>>>>>>
>>>>>> Cheers
>>>>>> Paulo
>>>>>>
>>>>>>> capabilities()
>>>>>> jpeg png tiff tcltk X11 aqua http/ftp sockets
>>>>>> TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE
>>>>>> libxml fifo cledit iconv NLS profmem cairo
>>>>>> TRUE TRUE TRUE TRUE TRUE FALSE TRUE
>>>>>>
>>>>>>
>>>>>>
>>>>>>> sessionInfo()
>>>>>> R version 2.12.1 (2010-12-16)
>>>>>> 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=C LC_MESSAGES=en_US.UTF-8
>>>>>> [7] LC_PAPER=en_US.UTF-8 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_2.7.0 arrayQualityMetrics_3.2.4
>>>>>> [3] vsn_3.18.0 affyPLM_1.26.0
>>>>>> [5] preprocessCore_1.12.0 gcrma_2.22.0
>>>>>> [7] affy_1.28.0 Biobase_2.10.0
>>>>>>
>>>>>> loaded via a namespace (and not attached):
>>>>>> [1] affyio_1.18.0 annotate_1.28.0 AnnotationDbi_1.12.0
>>>>>> [4] beadarray_2.0.3 Biostrings_2.18.2 DBI_0.2-5
>>>>>> [7] genefilter_1.32.0 grid_2.12.1 hwriter_1.3
>>>>>> [10] IRanges_1.8.8 KernSmooth_2.23-4 lattice_0.19-13
>>>>>> [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0
>>>>>> [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1
>>>>>> [19] splines_2.12.1 stats4_2.12.1 survival_2.36-2
>>>>>> [22] SVGAnnotation_0.7-2 tools_2.12.1 XML_3.2-0
>>>>>> [25] xtable_1.5-6
>>>>>>
>>>>>> _______________________________________________
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>>>>>> Bioconductor at r-project.org
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>>>>>>
>>>>
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>>>
>>>
>>> --
>>>
>>>
>>> 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
>
>
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