CODEWITHSUNDEEP
pythoninstallationscipyosx-maverickshomebrew
shadowtalker
shadowtalker

Reputation: 13883

Mavericks: brew install scipy -- okay, brew test scipy -- failure

I followed the suggestion here for installing SciPy on Mavericks and ran:

brew install python3

pip3 install virtualenv nose

brew install numpy --with-python3
brew install scipy --with-python3

brew test numpy
brew test scipy

and didn't run into any trouble until the last command, which produced:

Testing scipy
==> python -c import scipy; assert not scipy.test().failures
Python version 2.7.5 (default, Mar  9 2014, 22:15:05) [GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)]
nose version 1.3.4
Traceback (most recent call last):
  File "<string>", line 1, in <module>
AssertionError
Error: scipy: failed
Failed executing: python -c import\ scipy;\ assert\ not\ scipy.test().failures
/usr/local/Library/Homebrew/formula.rb:585:in `system'
/usr/local/Library/Taps/homebrew/homebrew-python/scipy.rb:78:in `block (2 levels) in <class:Scipy>'
/usr/local/Library/Homebrew/language/python.rb:25:in `call'
/usr/local/Library/Homebrew/language/python.rb:25:in `block in each_python'
/usr/local/Library/Homebrew/language/python.rb:17:in `each'
/usr/local/Library/Homebrew/language/python.rb:17:in `each_python'
/usr/local/Library/Taps/homebrew/homebrew-python/scipy.rb:77:in `block in <class:Scipy>'
/usr/local/Library/Homebrew/formula.rb:509:in `block in run_test'
/usr/local/Library/Homebrew/extend/fileutils.rb:21:in `mktemp'
/usr/local/Library/Homebrew/formula.rb:507:in `run_test'
/usr/local/Library/Homebrew/cmd/test.rb:59:in `block (2 levels) in test'
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/timeout.rb:66:in `timeout'
/usr/local/Library/Homebrew/cmd/test.rb:58:in `block in test'
/usr/local/Library/Homebrew/cmd/test.rb:37:in `each'
/usr/local/Library/Homebrew/cmd/test.rb:37:in `test'
/usr/local/Library/brew.rb:136:in `<main>'

And when I open python3 and type import scipy; scipy.test() I get hundreds of errors and dozens of failed tests:

FAILED (KNOWNFAIL=276, SKIP=920, errors=326, failures=42)
<nose.result.TextTestResult run=16412 errors=326 failures=42>

What did I do wrong? I had previously installed a bunch of software (like Python), then uninstalled everything and started over, but probably didn't do it so cleanly. Can I salvage this without reinstalling Mavericks?

Meanwhile, Homebrew installed GCC 4.9 as a dependency of NumPy, but that output suggests I'm still using whatever I had installed with XCode. This could be a separate issue, but gcc -v gives me:

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin13.4.0
Thread model: posix

The reason I mention it is that I'd like to know if I caused a bigger problem with my system.

Upvotes: 0

Views: 458

Answers (2)

Tim Smith
Tim Smith

Reputation: 6349

These errors are spurious and may be ignored. This will be fixed in an upcoming release of scipy. The scipy issue explaining this problem is here: https://github.com/scipy/scipy/issues/3853

The Homebrew-python scipy formula now applies the same fix that scipy will apply in the next release; after brew update && brew reinstall scipy, brew test scipy will pass.

Upvotes: 2

David Schlesinger
David Schlesinger

Reputation: 91

I've run into the same issue using Python 2.7. I've tried a couple of different things:

  • creating a soft link named "gcc" to gcc-4.9 in /usr/local/bin so that the brewed version shows up when I do a which gcc

    sudo ln -s /usr/local/Cellar/gcc/4.9.2/bin/gcc-4.9 /usr/local/bin/gcc

  • telling brew to use the default FORTRAN flags:

    brew install scipy --default-fortran-flags

I'm still getting the same error as the one you describe in response to brew test scipy. Running numpy's test suite produced no errors.

Upvotes: 0

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