[BioC] arrayQualityMetrics error
Paulo Nuin
nuin at genedrift.org
Sun Feb 13 00:16:46 CET 2011
Hi Wolfgang
I'm not able to install a newer version on my CentOS. The only official package for Cairo is 1.2.4. I didn't find a way to compile R and point it to a locally compiled Cairo (in /opt) and I don't know if it's possible to manage the compilation of packages in order to use this Cairo compile too.
Thanks
Paulo
On 2011-02-12, at 12:30 PM, Wolfgang Huber wrote:
> Dear Paulo
>
> Can you try with a more recent "Cairo" package (i.e. 1.4-6)?
>
> Wolfgang
>
> Il Feb/12/11 3:29 PM, Paulo Nuin ha scritto:
>> 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
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>>>>>>>> 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
>>>
>>>
>>
>
> --
>
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
>
>
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