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

Ralf Gommers ralf.gommers@googlemail....
Sat Feb 18 06:46:35 CST 2012


On Mon, Feb 13, 2012 at 5:58 PM, Paul Anton Letnes <
paul.anton.letnes@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
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