[BioC] Failed installing SJava on MacOS (success!)

Michael Dondrup Michael.Dondrup at uni.no
Fri Jan 22 17:09:56 CET 2010

yes I was a bit puzzled, but now I got it working in R, R GUI and R64 GUI. Maybe there is still
a glitch because you have to install three times for each binary but....

See below: 


Am Jan 22, 2010 um 4:34 PM schrieb Steve Lianoglou:

> Hi,
> On Fri, Jan 22, 2010 at 6:02 AM, Michael Dondrup <Michael.Dondrup at uni.no> wrote:
>> Dear Seth and Martin,
>> this is great news. Thank you very much for this effort. I tried it and it works without problem in R started in  a terminal.
>> If I use the R-GUI however, I get:
>> [R.app GUI 1.31 (5537) i386-apple-darwin9.8.0]
>>> library(SJava)
>> Error: package 'SJava' is not installed for 'arch=i386'
>> That's where it doesnt work:
> <snip>
>> Looks like another architecture dependent issue, as if this code is only installed for the 64bit version of R.
>> Anyway, it is really great that it's working, so I can try advance to use RWebServices :)
>> Whenever I can test something, pls let me know.
> 1. How did you install it? I think there are probably some flags you
> can set to have it compile both 64 and 32 bit versions (but I'm kind
> of surprised that this didn't happen automatically ...

Yes, I have never seen this with any other package, I installed from the commandline:
sudo R CMD INSTALL --clean SJava 
after that it works with /usr/bin/R
but in the GUI I get: 
[R.app GUI 1.31 (5537) i386-apple-darwin9.8.0]
> library(SJava)
Error: package 'SJava' is not installed for 'arch=i386'
And more striking in the R64 GUI I got:
[R.app GUI 1.31 (5537) x86_64-apple-darwin9.8.0]
> library(SJava)
Error: package 'SJava' is not installed for 'arch=x86_64'

So I installed the package using both /Applications/R and R64
Therefore I built a package with "R CMD build SJava" and installed it as a local package for the actual user (not gloabally). 

> 2. Why not just use the 64bit version of the R GUI as well? You can
> download it here:
> http://r.research.att.com/#GUI

I downloaded the R-2.10.1.pkg from cran, that also contained the R64, but I never used it because I use mainly the console.

> Download the version that that ends in *Leapard64.dmg that's also the
> right version of R that you're using, eg:
> http://r.research.att.com/R-GUI-5548-2.10-leopard-Leopard64.dmg
> Doing #2 is kind of side stepping the issue, but I think you'd
> probably like to run R/64bit even when running from the GUI as well.
> -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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