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

Michael Redmond redmond at cs.wisc.edu
Wed Nov 3 00:05:48 CET 2004

I will try the sourceforge g77 in place of the fink version. I am still 
hoping I can find someone that has prebuilt the BioC binaries I need.

It may be possible to run the XServe as a turnkey system, but for now it 
is going to be a fair amount of work to get R and Bioconductor into the 
portal interface. Once there, access is easy to manage. It is still 
likely that, even with the portal, some number of the research community 
here will want to run the XServe as a full Unix system, so then 
administation will be more typical of other systems.


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). 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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