[BioC] arrayQualityMetrics error

Wolfgang Huber whuber at embl.de
Sun Feb 13 12:22:37 CET 2011 

Paulo

perhaps you are trying to make things more complicated than necessary.
What happens when you enter

source("http://www.bioconductor.org/biocLite.R")
biocLite("Cairo")

into your R command line?

I am not sure what you mean by 'official package', the package page on 
CRAN, http://cran.r-project.org/web/packages/Cairo/index.html, provides 
1.4-6. I noted though that older versions are sticking around on the 
internet. Also note that the "Cairo" R package is not the same as the 
"cairo graphics library" e.g. at http://www.cairographics.org. You 
should not need to put anything into /opt or point R to it or anything 
like that.

	Best wishes
	Wolfgang






Il Feb/13/11 12:16 AM, Paulo Nuin ha scritto:
> 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
>>>>>>>>> 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
>>>>
>>>>
>>>
>>
>> --
>>
>>
>> Wolfgang Huber EMBL
>> http://www.embl.de/research/units/genome_biology/huber
>>
>>
>

-- 


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

More information about the Bioconductor mailing list