Using gcc45 from MATLAB: Incompatible library version

[infinity277]

Hi,

I get this error below when try to compile my code in Matlab.Why did this happen?

dyld: Library not loaded: /usr/local/opt/mpfr2/lib/libmpfr.1.dylib
  Referenced from: /usr/local/Cellar/gcc45/4.5.4/libexec/gcc/x86_64-apple-darwin13.4.0/4.5.4/cc1plus
  Reason: Incompatible library version: cc1plus requires version 4.0.0 or later, but libmpfr.1.dylib provides version 3.0.0
g++: Internal error: Trace/BPT trap: 5 (program cc1plus)

[apjanke]

Sounds like a mismatch between the dylib in the mpfr2 that gcc45 was built against, and the current installation of gcc45.

I did a fresh installation of gcc45 and mpfr2 on my 10.9.5 machine, and it seems to run without throwing that error.

$ /usr/local/Cellar/gcc45/4.5.4/libexec/gcc/x86_64-apple-darwin13.4.0/4.5.4/cc1plus -v
ignoring nonexistent directory "/usr/local/Cellar/gcc45/4.5.4/include"
ignoring nonexistent directory "/usr/local/Cellar/gcc45/4.5.4/lib/gcc/x86_64-apple-darwin13.4.0/4.5.4/../../../../x86_64-apple-darwin13.4.0/include"

Try reinstalling them with brew reinstall mpfr2 gcc45 and see if that fixes it. If not, please include the command you are running that's erroring out, and the output of brew doctor, brew config, brew info gcc45, and brew info mpfr2 (preferably all as a gist) so we can reproduce this and help you fix it.

[infinity277]

Hi,

I try to reinstall mpfr2 gcc45 but the error still appear in Matlab.
This appeared when I typed try brew info mpfr2

homebrew/versions/mpfr2: stable 2.4.2 (bottled) [keg-only]
Multiple-precision floating-point computations C lib
http://www.mpfr.org/
/usr/local/Cellar/mpfr2/2.4.2 (24 files, 2.7M)
Poured from bottle
From: https://github.com/Homebrew/homebrew-versions/blob/master/mpfr2.rb
==> Dependencies
Required: gmp4 ✔
==> Options
--with-32-bit

==> Caveats
This formula is keg-only, which means it was not symlinked into /usr/local.

Conflicts with mpfr in main repository.

Generally there are no consequences of this for you. If you build your
own software and it requires this formula, you'll need to add to your
build variables:

LDFLAGS:  -L/usr/local/opt/mpfr2/lib
CPPFLAGS: -I/usr/local/opt/mpfr2/include

[apjanke]

What are you doing in Matlab that ends up calling this? I have a Matlab license, so I may be able to reproduce it, if you can supply enough details.

Could you also post the output of brew config and brew doctor?

[infinity277]

I try to compile SPArse Modeling Software(http://spams-devel.gforge.inria.fr/downloads.html) in Matlab.

brew config
HOMEBREW_VERSION: 0.9.9
ORIGIN: https://github.com/Homebrew/brew
HEAD: df489cf
Last commit: 2 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 2443bf5
Core tap last commit: 5 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: quad-core 64-bit haswell
OS X: 10.9.5-x86_64
Xcode: 6.2
CLT: 6.2.0.0.1.1424975374
Clang: 6.0 build 600
X11: N/A
System Ruby: 2.0.0-p481
Perl: /usr/bin/perl
Python: /usr/bin/python
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby
Java: 1.6.0_65-b14-462
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

brew doctor
Warning: Some directories in /usr/local/share/man aren't writable.
This can happen if you "sudo make install" software that isn't managed
by Homebrew. If a brew tries to add locale information to one of these
directories, then the install will fail during the link step.

You should probably sudo chown -R $(whoami) them:
/usr/local/share/man/de
/usr/local/share/man/de/man1

[UniqMartin]

What version of MATLAB are you using? You're most likely running into this issue because MATLAB is bundling its own version of libmpfr and that version gets precedence. You either need to build outside of MATLAB or (preferably) use Clang as that's the only officially supported compiler for MATLAB on OS X.

[infinity277]

I used Matlab 2013a(version 8.1.0.064)

[UniqMartin]

MATLAB R2013a internally uses a shell script to set up its environment before it starts the graphical user interface. One of the environment variables being set is DYLD_LIBRARY_PATH and one of the paths contained in this variable is /Applications/MATLAB_R2013a.app/bin/maci64. This directory contains an older version of libmpfr.1.dylib. Because DYLD_LIBRARY_PATH takes precedence above the paths recorded inside a binary like cc1plus, it tries to load the library that is part of MATLAB (because it has the same file name) instead of the one installed by Homebrew. You can check the contents of that environment variable from within MATLAB:

getenv('DYLD_LIBRARY_PATH')

That's an issue specific to MATLAB and unfortunately there's nothing Homebrew can do about this. I'd strongly suggest to use Clang (as that's the only officially supported compiler by MathWorks on OS X). If that's not possible, because you need OpenMP and/or FORTRAN support, you can try building outside of MATLAB or you can try resetting DYLD_LIBRARY_PATH from withing MATLAB by running

setenv('DYLD_LIBRARY_PATH', '')

before trying to use gcc45. Hopefully one of those ideas works for you. Good luck!

Closing, as this is not an issue with Homebrew.