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


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