[BioC] Wow, what have I done

[Kasper Daniel Hansen]

On Dec 10, 2007, at 5:29 PM, Loren Engrav wrote:

> So I did and this is half Mac list half Bio list
>
> curl -O http://r.research.att.com/exp/R-2.3.1-ppc64.tar.gz
> sudo tar fvxz R-2.3.1-ppc64.tar.gz -C /
> sudo ln -sf /usr/local/lib64/R/bin/R /usr/local/bin/R64
>
> As per <http://cran.fhcrc.org/>
>
> And cool, I have 64 bit R which launches

But your R version is 2.3.1 - seriously outdated.

You should be using the build of R-2.6.1 that says "leopard only,  
pp64" on
http://r.research.att.com/
You need to be using leopard

(I hope you are using a G5 cpu, otherwise it will not work, I can see  
from earlier posts that you are using a PowerPC cpu).

Then you need to do
  options(pkgType = "source")
and set up your mac to install bioconductor from source (otherwise  
you will not get 64bit versions of the packages, which is what you  
want). This may be painful if you have not done so before. Them you  
can do
  biocLite()

It is possible as far as I know to get 64bit R to run under Tiger,  
but it is supposedly very painful. The stuff above requires you to  
upgrade to Leopard however.

Kasper


> But the
>
> source("http://bioconductor.org/biocLite.R")
> biocLite()
>
>  method of installing packages failed with complicated error messages
>
> So I obtained the monster 64bit package from <http://cran.fhcrc.org/>
>  and dragged it all into the various /usr folders
>
> And super,
> ReadAffy now reads 81 .cel files no problem with 2.5 gig
> So the 64bit is far more efficient than the 32bit
>
> But now 3 new questions
> 1) does the biocLite method of packages work with R64bit
> 2) affyQCReport is not in the monster, how do I get affyQCReport  
> into 64 bit
> 3) when quitting R in the Terminal (Mac) I save the image but do  
> not know
> where it went nor what it is named, where is it, what is it called
>
> Thank you
>
> -- 
> Loren Engrav
> Univ Washington
> Seattle
>
>> From: "Marcus G. Daniels" <mdaniels at lanl.gov>
>> Date: Mon, 10 Dec 2007 12:15:53 -0700
>> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>> Subject: Re: [BioC] Wow, what have I done
>>
>> Loren Engrav wrote:
>>> 3) try 64bit R
>>>
>> Also if you are a Linux user, you can try VMware Fusion together with
>> some x86_64 distribution of Linux (e.g. Fedora 8 x86_64 has a 64  
>> build
>> of R). This will get you up past the 4GB software limit (up to 8GB
>> virtual memory).
>>
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>
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