[R-SIG-Mac] JGR on Mac OS X 10.6 (Snow Leopard)

[Steve Lianoglou]

Hi Micahel,

On Sep 14, 2009, at 8:44 AM, Michael Kubovy wrote:

> Hi Simon,
>
> I'm sorry to say that I've tried and failed to set up 64-bit R 2.9.2  
> and JGR.
>
> (1) It's not clear to me where on http://r.research.att.com/ to  
> download from. (I searched for "snow", since all else assumed that I  
> know what I'm doing.)

Look at this section:

Universal nightly builds for Mac OS X (10.4 Tiger and 10.5 Leopard)

For R-2.9.2, you want to look at the third row of that table:

R-2.9-branch
R 2.9.2 Patched (2009-09-05)

http://r.research.att.com/R-2.9-branch-leopard-universal.tar.gz

Note that this is NOT an installer, you have to untar the file and  
have it "inflate" at the root of your file system. The way to do that  
is explained immediately after that download/table listing:

"""Alternatively you can use the tar-ball (*.tar.gz) which must be  
unpacked in the root (e.g. tar fvxz R*.tar.gz -C /), but doesn't  
contain the GUI (see below for a separate download)."""

> (2) I don't understand why you say (below) to download 2.9.0 rather  
> than 2.9.2.

I don't know why he mentioned that, but if this is the case, look at  
the "Leopard Build" section, there is a *.pkg installer for 2.9.0

http://r.research.att.com/R-2.9.0.pkg

> So could you please give step by step fool-proof instructions?  
> (Right now, after fiddling, I can't launch R or JGR.)

Downloading and installing one of the two R versions above will at  
least get R back up and running on your system (from the terminal, at  
least -- perhaps the *.pkg has the R.app gui installed too, I'm not  
certain).

If R is completely hosed, you might want to start by removing all  
current installs (/Library/Frameworks/R.framework) you have now to  
ensure everything is fresh and clean (but maybe not, up to you.).

-steve

>
> Thanks,
> Michael
>
> On Sep 12, 2009, at 7:59 PM, Simon Urbanek wrote:
>
>> To answer all those recent posts on both mailing lists regarding  
>> JGR on OS X 10.6 (Snow Leopard):
>>
>> You need 64-bit R to run JGR, because Apple has removed 32-bit Java  
>> from OS X 10.6. So follow those steps:
>>
>> 1) Install 64-bit R from http://r.research.att.com/
>> option a) install R 2.9.0 package (but choose to NOT install  
>> gfortran)
>> option b) unpack the leopard tar ball for R 2.9.2 and get the GUI  
>> from
>> http://r.research.att.com/R-GUI-5473-2.9-leopard-Leopard64.dmg
>> (in fact you can do both if you wish... ;))
>>
>> 2) install necessary packages as follows:
>> install.packages(c("rJava","JavaGD","iplots"))
>> install.packages("JGR",type="mac.binary")
>>
>> 3) download 64-bit JGR launcher from
>> http://urbanek.info/JGR-1.6-SL.dmg
>>
>> Run the launcher and enjoy.
>>
>> ---
>>
>> If you want to use JGR 1.7 from RForge.net, you have to install the  
>> packages from sources (when building JGR you must set NOAWT=1).
>> If you are using your own build of R, you must build everything  
>> from sources yourself.
>>
>> Cheers,
>> Simon
>>
>
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--
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