[BioC] Fwd: Wow, what have I done

[Loren Engrav]

Cool, thank you
So I bagged 2.3.1 and
Got up a big drive and
Put up Leopard and
Installed R-2.6-branch-leopard-universal.tar.gz
and

R --arch=ppc64 in the terminal now seems to work tho I have not done
ReadAffy on 81 cels yet and affyQCReport

How does one make R.app do R --arch=ppc64?

Google for R.app ppc64 failed me

This thread might be Mac not Bio but the goal is ReadAffy 81 cels so this is
where it started

Thank you

-- 
Loren Engrav
Univ Washington
Seattle




> From: Herve Pages <hpages at fhcrc.org>
> Date: Tue, 11 Dec 2007 19:07:52 -0800
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Fwd:  Wow, what have I done
> 
> 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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>