[R-SIG-Mac] Installing Bioconductor 1.5 on R 2.0 for OS X

[Byron Ellis]

On Nov 2, 2004, at 2:11 PM, Michael Redmond wrote:

> I have a working version of R 2.0 with option packages installed on an 
> OS X 10.3.5 system. Option packages were installed with 
> install.binaries option and that seemed to work. Install using sources 
> failed.
>
> I tried installing bioconductor from sources and got mixed results (at 
> best). Some packages failed to install (annotate, graph, Rgraphviz and 
> maybe XML and possibly others). I also need to install arrayCGH to get 
> DNAcopy. That uses the g77 compiler and failes with a mismatch of gcc 
> library versions. I have g77 from fink.

You want the g77 from http://hpc.sourceforge.net---the fink g77 has 
never worked properly for me (actually, thats a general statement about 
fink for me :-) )

>
> Is there a install.binary option for bioconductor and some of the 
> bioconductor contributed packages (specifically  arrayCGH)? If not 
> now, when (if ever). If never, I may need some help to fix compile 
> errors trying from source.
>

Jan De Leeuw usually wraps up the latest Bioconductor release into his 
"Batteries Included" version of R. I don't think there's a dedicated OS 
X machine doing binary builds anymore (IIRC, there used to be one doing 
the nightly smoke test). Unfortunately, OS X is probably the most 
finicky platform at the moment as well for that reason.

> I am working on this for an Apple 4 node XServe to see if it can be 
> used  under the iNquiry portal for R/Bioconductor applications.

Ooh! Could you ping me off list about how thats working out for you? 
Our group has been considering one to serve some of internal 
computational needs---we're mostly curious about how much 
administration and configuration it requires. (i.e., do you just turn 
it on and go?)

>
> Thanks
> Mike Redmond
> UW-Madison Statistics
>
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---
Byron Ellis (ellis at stat.harvard.edu)
"Oook" -- The Librarian