[BioC] arrayQualityMetrics error

Wolfgang Huber whuber at embl.de
Sat Feb 12 18:30:40 CET 2011 

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

More information about the Bioconductor mailing list