[BioC] arrayQualityMetrics error
Paulo Nuin
nuin at genedrift.org
Sun Feb 13 19:36:20 CET 2011
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
>
>
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