[BioC] arrayQualityMetrics error

Wolfgang Huber whuber at embl.de
Sun Feb 13 23:46:38 CET 2011 

Dear Paulo

sorry - that was my mistake. You were right to ask that question. I had 
overlooked that the source version of the Cairo R package *does* of 
course look for cairo libraries on your system.

I don't have a CentOS system to test this, but assuming that you use 
bash, have you tried something like:

env CAIRO_CFLAGS="-D_REENTRANT -I/opt/local/include/cairo 
-I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include 
-I/opt/local/include -I/opt/local/include/pixman-1 
-I/opt/local/include/freetype2 -I/opt/local/include/libpng14" 
CAIRO_LIBS="-L/opt/local/lib -lfreetype -lpng14 -lz -lXrender -lcairo 
-lX11" R CMD INSTALL Downloads/Cairo_1.4-6.tar.gz

This is all in one line, and the values between the "..." apply to my 
(Mac OS X with Mac ports) system, you'd need to replace the paths and 
library names with those applicable on your CentOS.

Sorry that this is so painful...

	Wolfgang


Il Feb/13/11 7:36 PM, Paulo Nuin ha scritto:
> Hi Wolfgang
>
> I know what you mean. If I try to install Cairo (the BioC package) it compiles fine, but it still relies on the cairographics that it's installed in the system:
>
>> biocLite("Cairo")
> ...
> checking for configurable backends... cairo cairo-ft cairo-pdf cairo-png cairo-ps cairo-xlib cairo-xlib-xrender
> configure: CAIRO_CFLAGS=-I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng12
> …
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Cairo.so cairobem.o cairogd.o cairotalk.o img-backend.o img-jpeg.o img-tiff.o pdf-backend.o ps-backend.o svg-backend.o w32-backend.o xlib-backend.o -lfreetype -lfontconfig -lpng12 -lz -lXrender -lcairo -lX11 -ljpeg -ltiff
> installing to /home/nuin/R/x86_64-unknown-linux-gnu-library/2.13/Cairo/libs
> ** R
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
>
> * DONE (Cairo)
>
> CentOS "official" cairographics is 1.2.4, which is quite old. I'm not able to install a newer cairographics in /usr or I can break my system. I can compile another newer version of cairographics on /opt, but them I would have to make the BioC's Cairo to point to /opt include and library dirs.
>
> Thanks again
>
> Paulo
>
>
>
> On 2011-02-13, at 6:22 AM, Wolfgang Huber wrote:
>
>> 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
>>
>>
>

-- 


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

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