[BioC] arrayQualityMetrics error
Paulo Nuin
nuin at genedrift.org
Thu Feb 10 21:11:19 CET 2011
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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>>
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>
>
> --
>
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
>
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