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building R from source

5 messages · Rafael Irizarry, Duncan Murdoch, stefano iacus +1 more

Original
Rafael Irizarry
# 
Hi!

I need to build R from source on my intel macbook pro. i am wondering if 
there is a consensus on what gcc and fortan to use.
Ive read the FAQ and various posts but there does not seem to be a 
specific rec.

I am looking for a specific rec because sometime ago I successfully 
installed R by using the gcc and gfortran described here 
http://hpc.sourceforge.net/ but I think this caused problems later. 
After the install, I had various weird issues that  other macbook pro 
users i knew did not have. One of the problems was that ssh seg faulted 
after the 10.4.8. upgrade. The only difference I could find between me 
and others was the aforementioned install. After two days of trying to 
fix the seg fault I gave up and re-installed the operating system. ssh 
is working again after reproducing everything i did before except for 
the gcc/gfortran install.

Any recs will be greatly appreciated.

Best wishes,
Rafael
Duncan Murdoch
#
On 2/11/2007 12:02 PM, Rafael Irizarry wrote:
This page

http://r.research.att.com/

gives detailed recommendations.  They worked for me last year.

Duncan Murdoch
stefano iacus
# 
My latest try is to use apple gcc which comes with latest Developer  
Tools and fortran from hpc.sourceforge.net

stefano
On 11/feb/07, at 19:09, Duncan Murdoch wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      Rafael Irizarry
    

    

      
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Stefano, This worked. Here is exactly what I did:

1) Upgraded Xcode tools to 2.4.1 from 
http://developer.apple.com/tools/download/

2) Installed the R 2.4.1 binaries from CRAN (i downloaded the dmg) and 
followed the default install.

3) I installed gfortan by downloading this 
http://prdownloads.sourceforge.net/hpc/gfortran-intel-bin.tar.gz?download
and typing this:
sudo tar -xvzf gfortran-intel-bin.tar.gz -C /
as described here:
http://hpc.sourceforge.net/.

4) Downloaded the R 2.4.1 tar.gz file, untared, made a dir to store the 
files, and used this configure and make:

./configure --prefix=/Users/ririzarr/src/R-2.4.1 --with-blas='-framework 
vecLib' CC=/usr/local/gcc4.0/bin/gcc F77=/usr/local/bin/gfortran

make CPPFLAGS=-DNEED_EXTERN_PC

R now works and so does ssh and everything else.

Thank again,
-r

        
stefano iacus wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    
15 days later

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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On Feb 12, 2007, at 8:57 PM, Rafael Irizarry wrote:

        

            

      
      
      
    

        
For the record: ^^^-- this CPPFLAGS setting is needed *only* for the  
compilation of GNU readline, not for R.

            

      
      
      
    

        
As of your broken setup before - I do not recommend installing gcc  
from the HPC page, pick the gfortran compiler *only*. Even it has its  
issues, but at least it should not affect other (non-fortran) software.

BTW: as of broken system debugging: try setting  
DYLD_PRINT_LIBRARIES=1 before you start programs to see if they pick  
up libraries from wrong places. Also make sure DYLD_LIBRARY_PATH is  
not set, it causes a lot of headaches as it works in slightly  
unexpected (albeit well documented) ways.

Cheers,
Simon