[BioC] arrayQualityMetrics

Guillaume Meurice guillaume.meurice at igr.fr
Mon Apr 4 09:11:09 CEST 2011 

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
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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
> 
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