Hi Mark

When trying to install separatly Cairo and SVGAnnotation, I got the following error message : 

##################################################################################
source("http://www.bioconductor.org/biocLite.R")
biocLite('Cairo')
Using R version 2.13.0 (R-devel), biocinstall version 2.8.2.
Installing Bioconductor version 2.8 packages:
[1] "Cairo"
Please wait...

trying URL 'http://mirror.ibcp.fr/pub/CRAN/src/contrib/Cairo_1.4-8.tar.gz'
Content type 'application/x-gzip' length 78688 bytes (76 Kb)
opened URL
==================================================
downloaded 76 Kb

configure: error: Cannot use cairo-ft backend, although cairo claims it is working. Please check your caito installation and/or update cairo if necessary or set CAIRO_CFLAGS/CAIRO_LIBS accordingly.
ERROR: configuration failed for package 'Cairo'
* removing '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Cairo'

##################################################################################



and for SVGAnnotation (that seems to need Cairo to be installed)

##################################################################################
source("http://www.bioconductor.org/biocLite.R")
biocLite("SVGAnnotation")
Using R version 2.13.0 (R-devel), biocinstall version 2.8.2.
Installing Bioconductor version 2.8 packages:
[1] "SVGAnnotation"
Please wait...

trying URL 'http://www.bioconductor.org/packages/2.8/extra/src/contrib/SVGAnnotation_0.9-0.tar.gz'
Content type 'application/x-gzip' length 4706070 bytes (4.5 Mb)
opened URL
==================================================
downloaded 4.5 Mb

During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_TIME failed, using "C" 
3: Setting LC_MESSAGES failed, using "C" 
* installing *source* package 'SVGAnnotation' ...
> q(status = capabilities()["cairo"] == FALSE)
*****   Using the Cairo package.
configure: creating ./config.status
config.status: creating DESCRIPTION
config.status: creating R/config.R
** R
** data
** inst
** preparing package for lazy loading
Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
  there is no package called 'Cairo'
Error : package 'Cairo' could not be loaded
ERROR: lazy loading failed for package 'SVGAnnotation'
* removing '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/SVGAnnotation'
##################################################################################




Best regards,
--
Guillaume Meurice - PhD
Bioinformaticien

Le Apr 5, 2011 à 2:22 AM, Mark Cowley a écrit :

> Hi Guillame,
> what happens when you do this:
> source("http://www.bioconductor.org/biocLite.R")
> biocLite('Cairo')
> biocLite("SVGAnnotation")
> 
> Mark
> 
> On 05/04/2011, at 1:39 AM, Guillaume Meurice wrote:
> 
>> 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@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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>>> Bioconductor@r-project.org
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>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 
>> _______________________________________________
>> Bioconductor mailing list
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> 


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