[BioC] arrayQualityMetrics error

Wolfgang Huber whuber at embl.de
Thu Feb 10 21:19:59 CET 2011 

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
>>>>>
>>>>> _______________________________________________
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>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>>>>
>>>
>>> _______________________________________________
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>>
>>
>> --
>>
>>
>> Wolfgang Huber
>> EMBL
>> http://www.embl.de/research/units/genome_biology/huber
>>
>> _______________________________________________
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>

-- 


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

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