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

Michael Redmond redmond at stat.wisc.edu
Mon Nov 8 23:21:19 CET 2004

I have been having some success with R installation by replacing the 
fink version of g77 with the sourceforge version. So thanks very much 
for that info.

Now that I have a good R base system compiled on OS X (I am trying  both 
on a Powerbook for testing and on the XServe), I have been trying to 
load bioconductor to test compile with the sourceforge g77, but with no 
success over the last week. Something seems to have changed, since I was 
able to get further along before then.

On the Powebook, I do the standard connect to 
http://www.bioconductor.org/getBioC.R and the do the getBioC(). It spins 
for a few seconds, then gives an error message "Error in getBioC()" but 
with no additional diagnostic information. This is the same if I ask for 
default or specific packages. I also tried "verbose = TRUE" and got no 
additional info. When I try on the XServe, I get an error message "Error 
in file(file, "wb") : unable to open connection".

I am sure that I wasn't getting these messages when I first tried 
loading bioconductor to the XServe.

Any idea of what is up?
Mike Redmond
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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>> R-SIG-Mac at stat.math.ethz.ch
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> ---
> Byron Ellis (ellis at stat.harvard.edu)
> "Oook" -- The Librarian

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