[BioC] arrayQualityMetrics

[Wolfgang Huber]

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