Hi! On 20.09.2011, at 14:41, David Cournapeau wrote: > On Tue, Sep 20, 2011 at 5:13 AM, Samuel John <sc...@samueljohn.de> wrote: >> Ralf, thanks for your answer. >> >> However, in short: >> >> I want `pip install numpy; pip install scipy` to work on OS X Lion without >> extra effort :-) [...] > I will try to look at this problem next week, when I will receive a > new laptop with Lion on it. If I forget about it, please ping me at > the end of next week, we need to fix this,
Congratulation to your new Mac :-) When I download scipy.10.0b2 and get gfortran via homebrew: brew install gfortran (which is not the issue here) cd scipy-0.10.0b2 python setup.py build python setup.py install Then, scipy.test() causes segfaults or malloc errors: > samuel@ubi:~/Downloads/scipy-0.10.0b2 $ cd .. > samuel@ubi:~/Downloads $ ipython > Python 2.7.2 (default, Sep 16 2011, 11:18:55) > Type "copyright", "credits" or "license" for more information. > > IPython 0.11 -- An enhanced Interactive Python. > ? -> Introduction and overview of IPython's features. > %quickref -> Quick reference. > help -> Python's own help system. > object? -> Details about 'object', use 'object??' for extra details. > > In [1]: import scipy > > In [2]: scipy.test() > Running unit tests for scipy > NumPy version 1.6.1 > NumPy is installed in > /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy > SciPy version 0.10.0b2 > SciPy is installed in > /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy > Python version 2.7.2 (default, Sep 16 2011, 11:18:55) [GCC 4.2.1 (Based on > Apple Inc. build 5658) (LLVM build 2335.15.00)] > nose version 1.1.2 > ...................................................................................................................................................................................F.FSegmentation > fault: 11 > samuel@ubi:~/Downloads $ ipython > Python 2.7.2 (default, Sep 16 2011, 11:18:55) > Type "copyright", "credits" or "license" for more information. > > IPython 0.11 -- An enhanced Interactive Python. > ? -> Introduction and overview of IPython's features. > %quickref -> Quick reference. > help -> Python's own help system. > object? -> Details about 'object', use 'object??' for extra details. > > In [1]: import scipy > > In [2]: scipy.test() > Running unit tests for scipy > NumPy version 1.6.1 > NumPy is installed in > /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy > SciPy version 0.10.0b2 > SciPy is installed in > /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy > Python version 2.7.2 (default, Sep 16 2011, 11:18:55) [GCC 4.2.1 (Based on > Apple Inc. build 5658) (LLVM build 2335.15.00)] > nose version 1.1.2 > ...................................................................................................................................................................................F.FFPython(93907,0x7fff7201b960) > malloc: *** error for object 0x105ce5630: pointer being freed was not > allocated > *** set a breakpoint in malloc_error_break to debug > Abort trap: 6 However, when setting the CC, CXX and FFLAGS explicitly to avoid llvm: export CC=gcc-4.2 export CXX=g++-4.2 export FFLAGS=-ff2c python setup.py build python setup.py install Then scipy.test() works fine: > In [2]: scipy.test() > Running unit tests for scipy > NumPy version 1.6.1 > NumPy is installed in > /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy > SciPy version 0.10.0b2 > SciPy is installed in > /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy > Python version 2.7.2 (default, Sep 16 2011, 11:18:55) [GCC 4.2.1 (Based on > Apple Inc. build 5658) (LLVM build 2335.15.00)] > nose version 1.1.2 > ............................................................................................................................................................................................................................K............................................................................................................/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/interpolate/fitpack2.py:674: > UserWarning: > The coefficients of the spline returned have been computed as the > minimal norm least-squares solution of a (numerically) rank deficient > system (deficiency=7). If deficiency is large, the results may be > inaccurate. Deficiency may strongly depend on the value of eps. > warnings.warn(message) > ....../usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/interpolate/fitpack2.py:605: > UserWarning: > The required storage space exceeds the available storage space: nxest > or nyest too small, or s too small. > The weighted least-squares spline corresponds to the current set of > knots. > warnings.warn(message) > ........................K..K....../usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/numeric.py:1920: > RuntimeWarning: invalid value encountered in absolute > return all(less_equal(absolute(x-y), atol + rtol * absolute(y))) > ............................................................................................................................................................................................................................................................................................................................................................................................................................................/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/io/wavfile.py:31: > WavFileWarning: Unfamiliar format bytes > warnings.warn("Unfamiliar format bytes", WavFileWarning) > /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/io/wavfile.py:121: > WavFileWarning: chunk not understood > warnings.warn("chunk not understood", WavFileWarning) > 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Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/distributions.py:4110: RuntimeWarning: overflow encountered in exp > return exp(c*x-exp(x)-gamln(c)) > ................................./usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/distributions.py:4592: > RuntimeWarning: invalid value encountered in sqrt > vals = 2*(bt+1.0)*sqrt(b-2.0)/((b-3.0)*sqrt(b)) > .........................................................................................................................................................................................................................................................................................................S................................................................................................................................................................................................/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/stats/distributions.py:5107: > RuntimeWarning: divide by zero encountered in divide > return where((lam <= 0) | (abs(x) < 1.0/arr(lam)), Px, 0.0) > ....................................................................................................................................................................................................................................................................................................................................................................................................................... > ---------------------------------------------------------------------- > Ran 5651 tests in 53.627s > > OK (KNOWNFAIL=12, SKIP=36) > Out[2]: <nose.result.TextTestResult run=5651 errors=0 failures=0> Samuel _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion