[BioC] Fwd: Wow, what have I done

[Herve Pages]

Hi Loren,

Loren Engrav wrote:
> Thank you for trying to help, maybe I just do not get it
> 
> I am using the page you list below and then going to experimental 64 builds
> from that page

You don't need to follow this "Experimental 64-bit build of R" link (unless you want
to try to build this 64-bit R yourself). The R builds for Leopard are right there
on the page that people pointed to you, that is:

  http://r.research.att.com/

There are 4 different build flavors here: 2 for Tiger (for the i386 and ppc archs
only) and 2 for Leopard (these are _full_ universal builds aka "quad builds" i.e.
they were compiled for the 4 archs: i386, ppc, x86_64 and ppc64).

Now install either
	R-2.6-branch-leopard-universal.tar.gz
or
        R-devel-leopard-universal.tar.gz
depending on which version of BioC you want to use: the former is for BioC 2.1 (the
current release) and the latter for BioC 2.2 (the current devel).

Then start R with --arch=x86_64 or --arch=ppc64 and you will be running in 64-bit
mode. This is easy and should take you no more than 5-10 minutes.

> 
> There one finds one for Intel and one for PPC, both 10.4 (neither Leopard),
> Intel is 2.5.0 and PPC is 2.3.1
> 
> The monster package of R64 2.3.1 for PPC includes many Bio packages, but not
> affyQCReport

AFAIK, no build of R has ever contained any BioC package. You will need to install
them by following the very detailed instructions already given to you by Kasper.

H.


> 
> 
>> From: Sean Davis <sdavis2 at mail.nih.gov>
>> Date: Tue, 11 Dec 2007 19:48:57 -0500
>> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>> Subject: [BioC] Fwd:  Wow, what have I done
>>
>> Forgot to cc list on this one....
>>
>> On Dec 11, 2007 7:02 PM, Loren Engrav <engrav at u.washington.edu> wrote:
>>
>>> Thank you
>>> I tried and failed, you are right, I am confused
>>> Am using R64 2.3.1 and the monster pack since it is available and I have
>>> not
>>> installed Leopard as yet
>>> But R64 2.3.1 monster does not include affyQCReport and I have failed at
>>> loading it into R64 2.3.1 inspite of your trying to help
>>>
>>> By the way, if I get Leopard up this weekend, where is an R64 for Leopard
>>> with affyQCReport and affy?
>>>
>> Hi, Loren.
>>
>> R does not include any bioconductor packages--those need to be added after
>> installing R.
>>
>> You will need to install 64-bit R that goes with leopard.  I believe a link
>> was included earlier, but here it is: http://r.research.att.com/ .
>>
>> Then, you will need to follow the instructions for using biocLite that Herve
>> Pages sent (if I recall who sent it correctly).
>>
>> Sean
>>
>> [[alternative HTML version deleted]]
>>
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> 
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