[BioC] arrayQualityMetrics

Guillaume Meurice guillaume.meurice at igr.fr
Tue Apr 5 16:56:17 CEST 2011 

>> 2.) For Windows and Mac OS X users, Simon Urbanek also offers binary versions: http://cran.r-project.org/web/packages/Cairo/index.html .
>> As far as I understand (I have only tried on Windows, so please correct me if I am wrong for OS X) those already contain their own copy of the 'cairo' systems library, so they can just be installed from the R Gui and need no separate system level installation.
> 
> In this case, I was not able to install "Cairo" R package, the error message was the following : 
> 
> ##########################################################################
> 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'
##########################################################################

Here 's the answer from S. Urbanek about the installation of the R package "Cairo" for 64-bit build :
"""
Fair enough - the 64-bit iconv has different symbols than at the time ft was built so the 64-bit build fails. So for now you'll have to stick with R --arch i386 for the Cairo binary. In the meantime I'll see if I can build a fresh set of static ft that will work with the current iconv - it's a bit convoluted as we need a build that won't use CF so Cairo can be forked (for multicore, Rserve etc.).
Cheers,
Simon
"""


--
Guillaume Meurice - PhD
Bioinformaticien

Le Apr 5, 2011 à 3:18 PM, Guillaume Meurice a écrit :

> Dear Wolfgang,
> 
>> 1.) If you go the 'from source' route (which I personally prefer), then you will need to learn how to install system libraries and tools (e.g. compilers, make) on your computer; in this case, you will need to (properly) install the 'cairo' system library (not to be confused with the R package 'Cairo'). On Mac OS X, I and others have had good success using 'mac ports' (www.macports.org) for that.
> 
> After installing mac ports, I wasn't able to sync and selfupdate it, probably because I'm behind a very restricitive proxy at my work .... so I can't properly install cairo system library by this way.
> 
> 
>> 2.) For Windows and Mac OS X users, Simon Urbanek also offers binary versions: http://cran.r-project.org/web/packages/Cairo/index.html .
>> As far as I understand (I have only tried on Windows, so please correct me if I am wrong for OS X) those already contain their own copy of the 'cairo' systems library, so they can just be installed from the R Gui and need no separate system level installation.
> 
> In this case, I was not able to install "Cairo" R package, the error message was the following : 
> 
> ##########################################################################
> 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'
> ##########################################################################
> 
> I'll try to contact Simon Urbanek on R-SIG-MAC mailing list.
> 
> 
> Regards,
> --
> Guillaume Meurice - PhD
> Bioinformaticien
> 
>> 
>> Dear Guillaume
>> 
>> you're right, the Cairo package is the hard part, SVGAnnotation should install without further ado once you have Cairo. The error message that you have got is pretty explicit.
>> 
>> There are two ways to install R packages: from source, or precompiled binary versions.
>> 
>> 1.) If you go the 'from source' route (which I personally prefer), then you will need to learn how to install system libraries and tools (e.g. compilers, make) on your computer; in this case, you will need to (properly) install the 'cairo' system library (not to be confused with the R package 'Cairo'). On Mac OS X, I and others have had good success using 'mac ports' (www.macports.org) for that.
>> 
>> 2.) For Windows and Mac OS X users, Simon Urbanek also offers binary versions: http://cran.r-project.org/web/packages/Cairo/index.html .
>> As far as I understand (I have only tried on Windows, so please correct me if I am wrong for OS X) those already contain their own copy of the 'cairo' systems library, so they can just be installed from the R Gui and need no separate system level installation.
>> 
>> Hope this helps
>> 	Wolfgang
>> 
>> 
>> Guillaume Meurice scripsit 05/04/11 08:03:
>>> 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 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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>>>>> 
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>> 
>> 
>> -- 
>> 
>> 
>> Wolfgang Huber
>> EMBL
>> http://www.embl.de/research/units/genome_biology/huber
>> 
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