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

stefano iacus stefano.iacus at unimi.it
Wed Nov 3 00:35:43 CET 2004

On Nov 2, 2004, at 11:36 PM, Byron Ellis wrote:

> 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).

well, for 1.4 there are binary builds. For 1.5 I'm late, but it should 
be me again.
I'll setup everything back soon.

>  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
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