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

[stefano iacus]

On Nov 2, 2004, at 11:11 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.
hi Michael,

what exactly fails? You should set up the system as it is explained in 
the FAQ and g77 is one issue.
Are you using the getbioC script ? BioC 1.4 needs R 1.9.1 and 1.5 (to 
be released) needs R 2.0.0. You cannot use bioc 1.5 with 1.9.x

>
> 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.
>

I strongly suggest you one of the two options
1. build R from scratch eventually using fink stuff
2. remove any fink stuff, and use the cran binary of R 2.0.0.

> 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.
>

you should report the error logs to let us to help with these. I'm 
currently testing the build of BioC 1.5 using getBioC.
I'll put results here and on the bioc-related lists.

stefano


> 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.
>
> Thanks
> Mike Redmond
> UW-Madison Statistics
>
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