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Installing R from source: "../i386/ldpaths: No such file or directory"

5 messages · Marius Hofert, Simon Urbanek, Charlie Sharpsteen

Original
Marius Hofert
# 
Hi,

I tried to install R from source on a new MacBook Air running 10.7.1. I followed the steps in the R-Faq and did:

(1) installed Xcode 4.1
(2) installed a *corresponding* Fortran compiler from
http://r.research.att.com/tools -> "Apple Xcode gcc-42 add-ons" [the
correct version for Xcode 4.1 on Lion was gfortran-lion-5666-3.pkg]
(3.1) downloaded and unpacked the latest R sources from CRAN (R-2.13.2.tar.gz)
cd ~/Downloads
(3.2) chose the architecture (x86_64, i386, ppc or ppc64):
arch=x86_64
(3.3) created a build directory 
mkdir build
cd build
(3.4) configured R
../R-2.13.2/configure r_arch=$arch  CC="gcc -arch $arch" \
     CXX="g++ -arch $arch" F77="gfortran -arch $arch" \
     FC="gfortran -arch $arch" OBJC="gcc -arch $arch" \
     --x-includes=/usr/X11/include --x-libraries=/usr/X11/lib \
     --with-blas='-framework vecLib' --enable-BLAS-shlib --with-lapack
(3.5) built R
make -j8
(3.6) installed R in /Library/Frameworks
sudo make install
(4) made R visible from the command line
sudo ln -s /Library/Frameworks/R.framework/Resources/R /usr/local/bin/R 

Executing R in the shell (even after restart) brought:
bash-3.2$ R
/usr/local/bin/R: line 229: /Library/Frameworks/R.framework/Resources/etc/i386/ldpaths: No such file or directory

I found a similar something similar on https://stat.ethz.ch/pipermail/r-help/2007-December/147771.html but it was not answered. 

I check with the installation (from binaries) on another Mac. There the folder /Library/Frameworks/R.framework/Resources/etc contains "i386", "repositories", and "x86_64", but for the new installation, I only found subdirectories "repositories" and "x86_64". 


Cheers,

Marius
Marius Hofert
# 
Okay, I found out that I have to start R via "R --arch=x86_64", then I can start R. 
I simply created a shell alias and I can now just use "R". 

See also the full post: http://www.mail-archive.com/r-sig-mac at stat.math.ethz.ch/msg02207.html

Begin forwarded message:
Simon Urbanek
# 
Marius,
On Oct 2, 2011, at 9:11 AM, Marius Hofert wrote:

            

      
      
      
    

        
(FWIW: you don't need sudo if you are admin. If you use sudo once, you have to use it always.)

            

      
      
      
    

        
(FWIW: the canonical location is /Library/Frameworks/R.framework/Resources/bin/R)

            

      
      
      
    

        
The framework installation uses `arch` to determine the default architecture which in your case is i386 but it is not installed. You can edit

/Library/Frameworks/R.framework/Resources/bin/R

and replace 
: ${R_ARCH=/`arch`}
with
: ${R_ARCH=/x86_64}

The assumption is that if you use a framework the resulting R will be universal, but it your case it's not. I'll see if we can come up with something more robust ...

Cheers,
Simon

            

      
      
      
    

        
wrong list ;)

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      Charlie Sharpsteen
    

    

      
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On Sunday, October 2, 2011 8:12:20 AM UTC-7, Simon Urbanek wrote:

            

      
      
      
    

        
I run 10.6.8 with an x86_64 kernel and `arch` still returns i386 which is a 
bit misleading. For the Homebrew package manager, we decide if 64 bit 
binaries are preferred by checking the return value of `/usr/sbin/sysctl -n 
hw.cpu64bit_capable`.

-Charlie 
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      Simon Urbanek
    

    

      
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On Oct 3, 2011, at 4:12 PM, Charlie Sharpsteen wrote:

        

            

      
      
      
    

        
Yes, you can use `uname -m` to get the kernel preference.

            

      
      
      
    

        
Well, that is a bit misleading, too, because it assumes that 64-bit capable machines prefer 64-bit binaries, which is not always true (e.g. low-memory machines usually don't want the extra overhead).

The `arch` idiom was designed to tell PowerPC and Intel apart, it was not designed to detect preference between 32 and 64-bit - in fact 32-bit is more safe in that it will work anywhere (so far, I would not surprised if Apple changes that, too ;)).

Cheers,
Simon