[Rcppoctave-user] Apple Blues

[Renaud Gaujoux]

---------- Forwarded message ----------
From: Dominick Samperi <djsamperi at gmail.com>
Date: 30 October 2013 07:11
Subject: Apple Blues
To: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>


Hello Renaud,

I just tried unsuccessfully to upgrade my Apple desktop to
Mac OS X 10.9 (Mavericks), but due to a few technical
problems I had to backtrack to the previous version
10.8 for now.

After restoring from backups and checking
that everything works, I discovered that RcppOctave
does not install. I get the same invalid malloc error that
I was getting before. But this time I have not used
MacPorts at all, only Homebrew, and the version of
Octave is 3.6.4 as it should be.

(I am downloading source, not using install.packages(), because
the latter tends to download old archives.)

Indeed, with my fresh install of Mac OS X, with the
command line tools and Xcode installed, R does not
issue the correct command: R CMD config CXX
returns: llvm-g++-4.2 -arch x86_64.

But there is no llvm-g++-4.2, only /usr/bin/g++ (version
4.2.1) and /usr/bin/gcc (version 4.2.1). I tried to work-around
this problem by defining symbolic links llvm-g++-4.2 and
llvm-gcc-4.2 pointing to these files, but this does not work.

There are a couple of open issues:
1. Apple no longer ships binaries named llvm-g++-4.2 and
   llvm-gcc-4.2 (only g++ and gcc).
2. Apple no longer supports Fortran at all (the R core team
    provides gfortran-4.2…see R Mac OS FAQ).
3. 'brew install octave' does not show you what it is doing,
   and I think it may be using clang instead of gcc, clang++
   instead of g++.
4. The segfault error when I try to install RcppOctave is
    probably due to compiler version incompatibilities, either
    gcc-4.2 vs gcc-4.2.1, or more likely, gcc-4.2.1 vs clang, etc.

Thus under Mac OS X the correct long-term solution is to
stop using gcc/g++ and follow Apple in using clang/clang++.
In the mean time, Apple will make life difficult for people who
continue to use gcc/g++/gfortran! (There is an open source
project to write an LLVM Fortran front-end, but I don't know
what the status of that project is.)

Dominick
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