[BioC] arrayQualityMetrics

[Guillaume Meurice]

Dear Wolgang,

Now I have installed R 2.13 (also with R.app), I've tried to install arrayQualityMetrics:
=======================================
source("http://www.bioconductor.org/biocLite.R")
biocLite("arrayQualityMetrics")

Using R version 2.13.0 (R-devel), biocinstall version 2.8.2.
Installing Bioconductor version 2.8 packages:
[1] "arrayQualityMetrics"
Please wait...

also installing the dependencies 'IRanges', 'Biostrings', 'DBI', 'RSQLite', 'xtable', 'affyio', 'preprocessCore', 'gcrma', 'BeadDataPackR', 'AnnotationDbi', 'annotate', 'affy', 'affyPLM', 'beadarray', 'Biobase', 'Cairo', 'genefilter', 'Hmisc', 'hwriter', 'latticeExtra', 'limma', 'RColorBrewer', 'setRNG', 'simpleaffy', 'SVGAnnotation', 'vsn', 'XML'
=======================================

it fails, raising the following error:

ERROR: dependencies 'Cairo', 'SVGAnnotation' are not available for package 'arrayQualityMetrics'


Best regards,
--
Guillaume Meurice - PhD
Bioinformaticien



Le Apr 4, 2011 à 4:41 PM, Guillaume Meurice a écrit :

> How nice ! thanks you for the tricks.
> 
> --
> Guillaume Meurice - PhD
> Bioinformaticien
> Le Apr 4, 2011 à 4:09 PM, Steve Lianoglou a écrit :
> 
>> Hi Guillaume,
>> 
>> On Mon, Apr 4, 2011 at 7:06 AM, Guillaume Meurice
>> <guillaume.meurice at igr.fr> wrote:
>>> 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.
>> 
>> If you find that you'd rather use the R.app GUI with R-2.13, you can
>> grab it from here:
>> 
>> http://r.research.att.com/#GUI
>> 
>> Go to the select the one that's appropriate for your architecture.
>> 
>> -steve
>> 
>> -- 
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>> | Memorial Sloan-Kettering Cancer Center
>> | Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
> 
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