[BioC] arrayQualityMetrics
Guillaume Meurice
guillaume.meurice at igr.fr
Mon Apr 4 13:06:58 CEST 2011
Dear Wolfgang,
Actually I used to install R using only macosx binaries, so I'm not that familiar with compilation. Anyway I finally managed to install R2.13 (I was needed gfortran compiler that is not included within X developper tools). Unfortunately, R.app (from 2.12) doesn't work with R2.13 :-(.
But nevermind, I now have to test the 3.7.1 release of AQM, running R in console mode.
Regards,
--
Guillaume Meurice - PhD
Bioinformaticien
> Dear Guillaume
>
> it is likely that your compilation problem is not related to whether you use a current R-beta or you wait till 13th, i.e. it might just as well be worthwhile to solve it now.
>
> You could post a more precise description of your compilation problem here, or perhaps more appropriate, R-help.
>
> Best wishes
> Wolfgang.
>
>
>
> Guillaume Meurice scripsit 04/04/11 09:11:
>> Dear Wolfgang,
>>
>> thanks for your answer.
>>
>> Unfortunately, I was not able to install the R.2.13 beta release (compilation won't work know). I will have to wait for the stable release that seems to come up to the 13th of April (or I hope so).
>>
>>
>>
>> Best regards,
>> --
>> Guillaume Meurice - PhD
>> Bioinformaticien
>>
>> Unité de Génomique Fonctionnelle
>>
>> PR2 - Bureau 323.2
>> Poste : 3509
>>
>> Institut Gustave Roussy - PR2
>> 114 rue Edouard Vaillant - 94805 VILLEJUIF Cedex
>> tel : +33 (0)1 42 11 42 11 (poste 3509)
>> fax : +33 (0)1 42 11 62 67
>>
>> Le Apr 1, 2011 à 11:21 PM, Wolfgang Huber a écrit :
>>
>>> 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]]
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at r-project.org
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>>>
>>> --
>>>
>>>
>>> Wolfgang Huber
>>> EMBL
>>> http://www.embl.de/research/units/genome_biology/huber
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
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>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
> --
>
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
>
>
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