[R-SIG-Mac] Probleme with libpng

Prof Brian Ripley ripley at stats.ox.ac.uk
Thu Mar 31 09:59:34 CEST 2011 

Why do you think the KernSmooth package has anything to do with this?
(I am its maintainer and it does not used libpng.)  Load it first, and 
you should see that png() works when it is loaded.

Be careful when you make accusations on public fora that they are 
honest and truthful!

On Thu, 31 Mar 2011, Guillaume Meurice wrote:

> 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
>>>>
>>>> _______________________________________________
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>>>> R-SIG-Mac at r-project.org
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>>>>
>>>>
>>>
>>
>>
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>>
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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