[BioC] arrayQualityMetrics error

Wolfgang Huber whuber at embl.de
Sat Feb 12 00:21:10 CET 2011 

Dear Paulo

what's your sessionInfo()?

	Wolfgang

Il Feb/11/11 1:26 PM, Paulo Nuin ha scritto:
> 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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>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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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
>>
>>
>

-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber

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