[BioC] arrayQualityMetrics error
Paulo Nuin
nuin at genedrift.org
Sat Feb 12 15:29:47 CET 2011
Hi Wolfgang
Here's just after running ReadAffy:
> sessionInfo()
R version 2.13.0 Under development (unstable) (2011-01-30 r54169)
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] arrayQualityMetrics_3.4.8 affy_1.29.2
[3] Biobase_2.11.8
loaded via a namespace (and not attached):
[1] affyio_1.19.4 affyPLM_1.27.6 annotate_1.29.2
[4] AnnotationDbi_1.13.13 beadarray_2.1.10 Biostrings_2.19.9
[7] Cairo_1.4-5 cluster_1.13.2 DBI_0.2-5
[10] genefilter_1.33.0 grid_2.13.0 Hmisc_3.8-3
[13] hwriter_1.3 IRanges_1.9.21 lattice_0.19-17
[16] latticeExtra_0.6-14 limma_3.7.22 marray_1.29.1
[19] preprocessCore_1.13.5 RColorBrewer_1.0-2 RJSONIO_0.4-1
[22] RSQLite_0.9-4 setRNG_2009.11-1 splines_2.13.0
[25] survival_2.36-2 SVGAnnotation_0.7-2 tools_2.13.0
[28] vsn_3.19.3 XML_3.2-0 xtable_1.5-6
after running arrayQualityMetrics the only difference is the addition of hgu133plus2cdf_2.7.0 to the list.
Thanks again
Paulo
On 2011-02-11, at 6:21 PM, Wolfgang Huber wrote:
> 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
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>
>
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