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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--
Brian D. Ripley, rip...@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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