[BioC] arrayQualityMetrics

Wolfgang Huber whuber at embl.de
Mon Apr 4 11:30:47 CEST 2011 

Dear Guillaume

it is likely that your compilation problem is not related to whether you 
use a current R-beta or you wait till 13th, i.e. it might just as well 
be worthwhile to solve it now.

You could post a more precise description of your compilation problem 
here, or perhaps more appropriate, R-help.

	Best wishes
	Wolfgang.



Guillaume Meurice scripsit 04/04/11 09:11:
> Dear Wolfgang,
>
> thanks for your answer.
>
> Unfortunately, I was not able to install the R.2.13 beta release (compilation won't work know). I will have to wait for the stable release that seems to come up to the 13th of April (or I hope so).
>
>
>
> Best regards,
> --
> Guillaume Meurice - PhD
> Bioinformaticien
>
> Unité de Génomique Fonctionnelle
>
> PR2 - Bureau 323.2
> Poste : 3509
>
> Institut Gustave Roussy - PR2
> 114 rue Edouard Vaillant - 94805 VILLEJUIF Cedex
> tel	: +33 (0)1 42 11 42 11 (poste 3509)
> fax	: +33 (0)1 42 11 62 67
>
> Le Apr 1, 2011 à 11:21 PM, Wolfgang Huber a écrit :
>
>> Dear Guillaume
>>
>> it looks like your R installation is broken (the warning about libpng) and lacks the 'svg' device.
>>
>> Can you please try with installing R 2.13 (i.e. currently a prelease 'beta' version) and the current version of arrayQualityMetrics (http://www.bioconductor.org/help/bioc-views/devel/bioc/html/arrayQualityMetrics.html), which has greatly changed over that from the last release.
>>
>> 	Best wishes
>> 	Wolfgang
>>
>>
>>
>> Il Apr/1/11 9:14 AM, Guillaume Meurice ha scritto:
>>> Dear All,
>>>
>>> I have a problem with arrayQualityMetrics (see following code).
>>> I would be very grateful if you could provide me with any idea so I can fixe the problem.
>>> Thanks you by advance.
>>>
>>>
>>> R code that produce the problem :
>>> ####################################################################
>>>> a = sessionInfo()
>>>> arrayQualityMetrics(eSet, outdir="aqmRaw", do.logtransform=T)
>>> The directory 'aqmRaw' has been created.
>>> KernSmooth 2.23 loaded
>>> Copyright M. P. Wand 1997-2009
>>> (loaded the KernSmooth namespace)
>>> [[1]]
>>> libpng warning: Application was compiled with png.h from libpng-1.2.26
>>> libpng warning: Application  is  running with png.c from libpng-1.4.1
>>> libpng warning: Incompatible libpng version in application and library
>>>
>>> libpng warning: Application was compiled with png.h from libpng-1.2.26
>>> libpng warning: Application  is  running with png.c from libpng-1.4.1
>>> libpng warning: Incompatible libpng version in application and library
>>> Error in svg(file = svgtemp, h = h, w = w) :
>>>    cairo-based devices are not supported on this build
>>>
>>>>
>>>> b = sessionInfo()
>>>>
>>> ####################################################################
>>>
>>>
>>> Difference between 'a' and 'b' sessionInfo
>>> ####################################################################
>>>> summary(a)
>>>             Length Class  Mode
>>> R.version  13     -none- list
>>> platform    1     -none- character
>>> locale      1     -none- character
>>> basePkgs    7     -none- character
>>> otherPkgs   7     -none- list
>>> loadedOnly 23     -none- list
>>>> summary(b)
>>>             Length Class  Mode
>>> R.version  13     -none- list
>>> platform    1     -none- character
>>> locale      1     -none- character
>>> basePkgs    7     -none- character
>>> otherPkgs   7     -none- list
>>> loadedOnly 24     -none- list
>>>>
>>> ####################################################################
>>>
>>>
>>>
>>>
>>> the 'a' sessionInfo
>>> ####################################################################
>>> R version 2.12.2 (2011-02-25)
>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>
>>> locale:
>>> [1] C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] arrayQualityMetrics_3.2.4 vsn_3.18.0                affyPLM_1.26.0            preprocessCore_1.12.0     gcrma_2.22.0
>>> [6] affy_1.28.0               Biobase_2.10.0
>>>
>>> loaded via a namespace (and not attached):
>>>   [1] AnnotationDbi_1.12.0 Biostrings_2.18.2    DBI_0.2-5            IRanges_1.8.8        RColorBrewer_1.0-2   RSQLite_0.9-4
>>>   [7] SVGAnnotation_0.7-2  XML_3.2-0            affyio_1.18.0        annotate_1.28.0      beadarray_2.0.3      genefilter_1.32.0
>>> [13] grid_2.12.2          hwriter_1.3          lattice_0.19-17      latticeExtra_0.6-14  limma_3.6.9          marray_1.28.0
>>> [19] simpleaffy_2.26.1    splines_2.12.2       stats4_2.12.2        survival_2.36-5      xtable_1.5-6
>>>
>>>
>>> the 'b' sessionInfo
>>> ####################################################################
>>>> b
>>> R version 2.12.2 (2011-02-25)
>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>
>>> locale:
>>> [1] C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] arrayQualityMetrics_3.2.4 vsn_3.18.0                affyPLM_1.26.0            preprocessCore_1.12.0     gcrma_2.22.0
>>> [6] affy_1.28.0               Biobase_2.10.0
>>>
>>> loaded via a namespace (and not attached):
>>>   [1] AnnotationDbi_1.12.0 Biostrings_2.18.2    DBI_0.2-5            IRanges_1.8.8        KernSmooth_2.23-4    RColorBrewer_1.0-2
>>>   [7] RSQLite_0.9-4        SVGAnnotation_0.7-2  XML_3.2-0            affyio_1.18.0        annotate_1.28.0      beadarray_2.0.3
>>> [13] genefilter_1.32.0    grid_2.12.2          hwriter_1.3          lattice_0.19-17      latticeExtra_0.6-14  limma_3.6.9
>>> [19] marray_1.28.0        simpleaffy_2.26.1    splines_2.12.2       stats4_2.12.2        survival_2.36-5      xtable_1.5-6
>>>>
>>>
>>>
>>>
>>> --
>>> Guillaume
>>>
>>>
>>> 	[[alternative HTML version deleted]]
>>>
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>>
>> --
>>
>>
>> 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

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