[SciPy-Dev] [SciPy-User] ANN: SciPy 0.10.1 release candidate 1

Tue Feb 21 02:12:03 EST 2012

On 18. feb. 2012, at 13:46, Ralf Gommers wrote:

> 
> 
> On Mon, Feb 13, 2012 at 5:58 PM, Paul Anton Letnes <paul.anton.letnes at gmail.com> wrote:
> Hi,
> 
> I screwed up my previous e-mail (using my non-virtualenv, regular python) and I am trying again. These are the results on my machine - OS X 10.7.3, gcc 4.2 from apple, and gfortran 4.6.2 from Homebrew-alt.
> 
> Paul
> 
> Running unit tests for scipy
> NumPy version 1.6.1
> NumPy is installed in /Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy
> SciPy version 0.10.1rc1
> SciPy is installed in /Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/scipy
> Python version 2.7.2 (default, Oct  9 2011, 18:03:13) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
> nose version 1.1.2
> ............................................................................................................................................................................................................................K............................................................................................................/Users/paulanto/Skrot/src/scipy-test/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)
> ....../Users/paulanto/Skrot/src/scipy-test/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.................................................................................................................................................................................................................................................................................................................................................................................................................................................../Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/scipy/io/wavfile.py:31: WavFileWarning: Unfamiliar format bytes
>  warnings.warn("Unfamiliar format bytes", WavFileWarning)
> /Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/scipy/io/wavfile.py:121: WavFileWarning: chunk not understood
>  warnings.warn("chunk not understood", WavFileWarning)
> ....................................................................................F..FF......................................................................................................................................SSSSSS......SSSSSS......SSSS.....................FFF.........................................F....FF.......S............................................................................................................................................................................................................................................................K......................................................................................................................................................................................................SSSSS............S..............................................................................................................................................................................................
>  ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSSSSSSS.........../Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py:63: UserWarning: Single-precision types in `eigs` and `eighs` are not supported currently. Double precision routines are used instead.
>  warnings.warn("Single-precision types in `eigs` and `eighs` "
> ....F.F.....................F...........F.F..............................................................................................F........................F.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K...............................................................K.................................................................
>  ..........................................................................................KK.............................................................................................................................................................................................................................................................................................................................................................................................................................................K.K.............................................................................................................................................................................................................................................................................................................................................................................................K........K..............SSSSSSS.....................................................
>  .....................................................................................................S..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
> ======================================================================
> FAIL: test_asum (test_blas.TestFBLAS1Simple)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 58, in test_asum
>    assert_almost_equal(f([3,-4,5]),12)
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
>    raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal to 7 decimals
>  ACTUAL: 0.0
>  DESIRED: 12
> 
> ======================================================================
> FAIL: test_dot (test_blas.TestFBLAS1Simple)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 67, in test_dot
>    assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
>    raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal to 7 decimals
>  ACTUAL: 0.0
>  DESIRED: -9
> 
> ======================================================================
> FAIL: test_nrm2 (test_blas.TestFBLAS1Simple)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 78, in test_nrm2
>    assert_almost_equal(f([3,-4,5]),math.sqrt(50))
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
>    raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal to 7 decimals
>  ACTUAL: 0.0
>  DESIRED: 7.0710678118654755
> 
> ======================================================================
> FAIL: test_basic.TestNorm.test_overflow
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
>    self.test(*self.arg)
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py", line 581, in test_overflow
>    assert_almost_equal(norm(a), a)
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 452, in assert_almost_equal
>    return assert_array_almost_equal(actual, desired, decimal, err_msg)
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 800, in assert_array_almost_equal
>    header=('Arrays are not almost equal to %d decimals' % decimal))
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
>    raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal to 7 decimals
> 
> (mismatch 100.0%)
>  x: array(-0.0)
>  y: array([  1.00000002e+20], dtype=float32)
> 
> ======================================================================
> FAIL: test_basic.TestNorm.test_stable
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
>    self.test(*self.arg)
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py", line 586, in test_stable
>    assert_almost_equal(norm(a) - 1e4, 0.5)
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
>    raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal to 7 decimals
>  ACTUAL: -10000.0
>  DESIRED: 0.5
> 
> ======================================================================
> FAIL: test_basic.TestNorm.test_types
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
>    self.test(*self.arg)
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py", line 568, in test_types
>    assert_allclose(norm(x), np.sqrt(14), rtol=tol)
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
>    verbose=verbose, header=header)
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
>    raise AssertionError(msg)
> AssertionError:
> Not equal to tolerance rtol=2.38419e-06, atol=0
> 
> (mismatch 100.0%)
>  x: array(1.0842021724855044e-19)
>  y: array(3.7416573867739413)
> 
> ======================================================================
> FAIL: test_asum (test_blas.TestFBLAS1Simple)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 99, in test_asum
>    assert_almost_equal(f([3,-4,5]),12)
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
>    raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal to 7 decimals
>  ACTUAL: 0.0
>  DESIRED: 12
> 
> ======================================================================
> FAIL: test_dot (test_blas.TestFBLAS1Simple)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 109, in test_dot
>    assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
>    raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal to 7 decimals
>  ACTUAL: 0.0
>  DESIRED: -9
> 
> ======================================================================
> FAIL: test_nrm2 (test_blas.TestFBLAS1Simple)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 127, in test_nrm2
>    assert_almost_equal(f([3,-4,5]),math.sqrt(50))
>  File "/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
>    raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal to 7 decimals
>  ACTUAL: 0.0
>  DESIRED: 7.0710678118654755
> 
> I'm not sure what to make of these. I'm tempted to say that for now only the recommended gfortran is supported. There's too much going wrong on OS X Lion to be able to fix it all for 0.10.1.
> 
> For 0.11.0 we should attempt to get this fixed, including the llvm-gcc situation.
> 
> Can you check where that gfortran 4.6.2 actually comes from?
> 
> Ralf

The homebrew formula is here:
https://github.com/adamv/homebrew-alt/blob/master/duplicates/gcc.rb
and it looks like this line says where to download from:
  url 'http://ftpmirror.gnu.org/gcc/gcc-4.6.2/gcc-4.6.2.tar.bz2'

I'll try to build with the recommended gfortran-4.2 as you suggested. Several people have pointed out the issues haunting gfortran on OS X. Annoying...

Paul