[R-SIG-Mac] Probleme with libpng
Guillaume Meurice
guillaume.meurice at igr.fr
Thu Mar 31 09:24:44 CEST 2011
Dear All,
After several test, I finally found where was the problem : It came from a package called arrayQualityMetrics (arrayQualityMetrics_3.2.4).
When using an internal function of this package, another package is loaded : KernSmooth_2.23-4.
a is the summary of sessionInfo before launching aqm function of arrayQualityMetrics package
b is the summary of sessionInfo after launching aqm function of arrayQualityMetrics package
> 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
as one can see below, the only difference between the two is the KernSmooth package
I'm going to write to the authors of arrayQualityMetrics package so as they can update the KernSmooth package.
Cheers
PS : Below is the code launch :
> a = sessionInfo()
> a
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
>
>
> png("foo.png")
> plot(rnorm(150,3))
> dev.off()
null device
1
>
>
>
> pData = target[,c(2,3)]
> rownames(pData) = target$Cy3
> phenoData = new("AnnotatedDataFrame", data=pData)
>
> exprs = G$E
> colnames(exprs) = rownames(pData)
> eSet = new("ExpressionSet", exprs = exprs, phenoData = phenoData)
>
> 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()
> 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
Cheers,
--
Guillaume Meurice - PhD
> Dear Simon,
>
> thank for your answer.
>
> I was just tring to draw a png :
> ==================
> png("foobar.png")
> plot(rnorm(10,3))
> dev.off()
> =================
>
> which returns :
>
> =================
> 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
> =================
>
>
>
> Then, after reading your answer, I've restarted R to check all libraries and the problem seems to be solved .... even with all the library I was using ...
>
> Sorry for disturbing and many thanks :)
>
> Cheers
> --
> Guillaume Meurice - PhD
>
> Le Mar 30, 2011 à 5:06 PM, Simon Urbanek a écrit :
>
>> You'll need to supply more details. What are you exactly doing? (reproducible example!) Which packages are you using? (sessionInfo()!)
>> Cheers,
>> Simon
>>
>>
>> On Mar 30, 2011, at 10:56 AM, Guillaume Meurice wrote:
>>
>>> Dear all,
>>>
>>> I've recently upgrade R to :
>>>
>>> R 2.12.2 GUI 1.36 Leopard build 64-bit (5691)
>>>
>>> But now, I can't drow any png image, since I have this error message :
>>>
>>> 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
>>>
>>>
>>> What should I do ? Is there any macosX package compiled with libpng 1.4.1 ?
>>>
>>>
>>> Thanks by advance for any help you could provide.
>>> Best regards,
>>> --
>>> Guillaume Meurice - PhD
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>>
>>
>
>
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