Developers of Scientific Python

headers Ralf Gommers | 11 Feb 15:11

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On 2/11/2012 6:11 AM, Ralf Gommers wrote:
> Hi all,
>
> I am pleased to announce the availability of the first release candidate
> of SciPy 0.10.1. Please try out this release and report any problems on
> the scipy-dev mailing list. If no problems are found, the final release
> will be available in one week.
>
> Sources and binaries can be found at
> http://sourceforge.net/projects/scipy/files/scipy/0.10.1rc1/, release
> notes are copied below.
>
> Cheers,
> Ralf
>
>
> ==========================
> SciPy 0.10.1 Release Notes
> ==========================
>
> .. contents::
>
> SciPy 0.10.1 is a bug-fix release with no new features compared to 0.10.0.
>
> Main changes
> ------------
>
> The most important changes are::
>
> 1. The single precision routines of ``eigs`` and ``eigsh`` in
>     ``scipy.sparse.linalg`` have been disabled (they internally use double
>     precision now).
> 2. A compatibility issue related to changes in NumPy macros has been
> fixed, in
>     order to make scipy 0.10.1 compile with the upcoming numpy 1.7.0
> release.
>
>
> Other issues fixed
> ------------------
>
> - #835: stats: nan propagation in stats.distributions
> - #1202: io: netcdf segfault
> - #1531: optimize: make curve_fit work with method as callable.
> - #1560: linalg: fixed mistake in eig_banded documentation.
> - #1565: ndimage: bug in ndimage.variance
> - #1457: ndimage: standard_deviation does not work with sequence of indexes
> - #1562: cluster: segfault in linkage function
> - #1568: stats: One-sided fisher_exact() returns `p` < 1 for 0
> successful attempts
> - #1575: stats: zscore and zmap handle the axis keyword incorrectly
>
>
>

Hi Ralf,

looks good here (Windows, msvc9, MKL, numpy 1.6.1). Just one compile 
error related to the numpy macros: 
<https://github.com/scipy/scipy/pull/156>.

Christoph

On Sat, Feb 11, 2012 at 2:55 PM, Christoph Gohlke <cgohlke <at> uci.edu> wrote:
>
>
> On 2/11/2012 6:11 AM, Ralf Gommers wrote:
>> Hi all,
>>
>> I am pleased to announce the availability of the first release candidate
>> of SciPy 0.10.1. Please try out this release and report any problems on
>> the scipy-dev mailing list. If no problems are found, the final release
>> will be available in one week.
>>
>> Sources and binaries can be found at
>> http://sourceforge.net/projects/scipy/files/scipy/0.10.1rc1/, release
>> notes are copied below.
>>
>> Cheers,
>> Ralf
>>
>>
>> ==========================
>> SciPy 0.10.1 Release Notes
>> ==========================
>>
>> .. contents::
>>
>> SciPy 0.10.1 is a bug-fix release with no new features compared to 0.10.0.
>>
>> Main changes
>> ------------
>>
>> The most important changes are::
>>
>> 1. The single precision routines of ``eigs`` and ``eigsh`` in
>>     ``scipy.sparse.linalg`` have been disabled (they internally use double
>>     precision now).
>> 2. A compatibility issue related to changes in NumPy macros has been
>> fixed, in
>>     order to make scipy 0.10.1 compile with the upcoming numpy 1.7.0
>> release.
>>
>>
>> Other issues fixed
>> ------------------
>>
>> - #835: stats: nan propagation in stats.distributions
>> - #1202: io: netcdf segfault
>> - #1531: optimize: make curve_fit work with method as callable.
>> - #1560: linalg: fixed mistake in eig_banded documentation.
>> - #1565: ndimage: bug in ndimage.variance
>> - #1457: ndimage: standard_deviation does not work with sequence of indexes
>> - #1562: cluster: segfault in linkage function
>> - #1568: stats: One-sided fisher_exact() returns `p` < 1 for 0
>> successful attempts
>> - #1575: stats: zscore and zmap handle the axis keyword incorrectly
>>
>>
>>
>
> Hi Ralf,
>
> looks good here (Windows, msvc9, MKL, numpy 1.6.1). Just one compile
> error related to the numpy macros:
> <https://github.com/scipy/scipy/pull/156>.
>
> Christoph

Not directly to the thread

Christoph,
Thank you for providing Windows binaries.
You just rescued my incomplete ipython install by providing the only
pyzmq binaries for Python 2.6 that I could find.

Josef

> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev <at> scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev

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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

(scipy-test)i-courant /tmp/paulanto % python -c 'import numpy;import scipy;numpy.test(verbose=1);scipy.test(verbose=1)'
Running unit tests for numpy
NumPy version 1.6.1
NumPy is installed in /Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy
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
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................./Users/paulanto/Skrot/src/scipy-test/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)))
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K.................................................................................................K......................K...........FFFFFFF...F./Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/core/tests/test_umath_complex.py:364:
RuntimeWarning: invalid value encountered in sqrt
  z = np.sqrt(np.array(np.complex(-np.inf, np.nan)))
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
 ..............................................................................................................................................................................................
 ..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................S....................................................................................................................................................................................................................................................................................
 ..............................................................................................................................................................................................
 ...................................................................................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, 1, inf, inf, inf)
----------------------------------------------------------------------
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/numpy/core/tests/test_umath_complex.py",
line 578, in check_complex_value
    assert_equal(f(z1), z2)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 256, in assert_equal
    return assert_array_equal(actual, desired, err_msg, verbose)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 707, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 605, in assert_array_compare
    chk_same_position(x_id, y_id, hasval='nan')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 588, in chk_same_position
    raise AssertionError(msg)
AssertionError: 
Arrays are not equal

x and y nan location mismatch:
 x: array([ nan+infj])
 y: array((inf+infj))

======================================================================
FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, -1, inf, inf, inf)
----------------------------------------------------------------------
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/numpy/core/tests/test_umath_complex.py",
line 578, in check_complex_value
    assert_equal(f(z1), z2)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 256, in assert_equal
    return assert_array_equal(actual, desired, err_msg, verbose)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 707, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 605, in assert_array_compare
    chk_same_position(x_id, y_id, hasval='nan')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 588, in chk_same_position
    raise AssertionError(msg)
AssertionError: 
Arrays are not equal

x and y nan location mismatch:
 x: array([ nan+infj])
 y: array((inf+infj))

======================================================================
FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, 0.0, inf, inf, inf)
----------------------------------------------------------------------
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/numpy/core/tests/test_umath_complex.py",
line 578, in check_complex_value
    assert_equal(f(z1), z2)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 256, in assert_equal
    return assert_array_equal(actual, desired, err_msg, verbose)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 707, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 605, in assert_array_compare
    chk_same_position(x_id, y_id, hasval='nan')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 588, in chk_same_position
    raise AssertionError(msg)
AssertionError: 
Arrays are not equal

x and y nan location mismatch:
 x: array([ nan+infj])
 y: array((inf+infj))

======================================================================
FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, -0.0, inf, inf, inf)
----------------------------------------------------------------------
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/numpy/core/tests/test_umath_complex.py",
line 578, in check_complex_value
    assert_equal(f(z1), z2)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 256, in assert_equal
    return assert_array_equal(actual, desired, err_msg, verbose)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 707, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 605, in assert_array_compare
    chk_same_position(x_id, y_id, hasval='nan')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 588, in chk_same_position
    raise AssertionError(msg)
AssertionError: 
Arrays are not equal

x and y nan location mismatch:
 x: array([ nan+infj])
 y: array((inf+infj))

======================================================================
FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, inf, inf, inf, inf)
----------------------------------------------------------------------
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/numpy/core/tests/test_umath_complex.py",
line 578, in check_complex_value
    assert_equal(f(z1), z2)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 256, in assert_equal
    return assert_array_equal(actual, desired, err_msg, verbose)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 707, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 605, in assert_array_compare
    chk_same_position(x_id, y_id, hasval='nan')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 588, in chk_same_position
    raise AssertionError(msg)
AssertionError: 
Arrays are not equal

x and y nan location mismatch:
 x: array([ nan+infj])
 y: array((inf+infj))

======================================================================
FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, -inf, inf, inf, inf)
----------------------------------------------------------------------
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/numpy/core/tests/test_umath_complex.py",
line 578, in check_complex_value
    assert_equal(f(z1), z2)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 256, in assert_equal
    return assert_array_equal(actual, desired, err_msg, verbose)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 707, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 605, in assert_array_compare
    chk_same_position(x_id, y_id, hasval='nan')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 588, in chk_same_position
    raise AssertionError(msg)
AssertionError: 
Arrays are not equal

x and y nan location mismatch:
 x: array([ nan+infj])
 y: array((inf+infj))

======================================================================
FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, nan, inf, inf, inf)
----------------------------------------------------------------------
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/numpy/core/tests/test_umath_complex.py",
line 578, in check_complex_value
    assert_equal(f(z1), z2)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 256, in assert_equal
    return assert_array_equal(actual, desired, err_msg, verbose)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 707, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 605, in assert_array_compare
    chk_same_position(x_id, y_id, hasval='nan')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 588, in chk_same_position
    raise AssertionError(msg)
AssertionError: 
Arrays are not equal

x and y nan location mismatch:
 x: array([ nan+infj])
 y: array((inf+infj))

======================================================================
FAIL: test_umath_complex.TestCsqrt.test_special_values(<ufunc 'sqrt'>, -inf, 1, 0.0, inf)
----------------------------------------------------------------------
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/numpy/core/tests/test_umath_complex.py",
line 578, in check_complex_value
    assert_equal(f(z1), z2)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 256, in assert_equal
    return assert_array_equal(actual, desired, err_msg, verbose)
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 707, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 605, in assert_array_compare
    chk_same_position(x_id, y_id, hasval='nan')
  File
"/Users/paulanto/Skrot/src/scipy-test/lib/python2.7/site-packages/numpy/testing/utils.py",
line 588, in chk_same_position
    raise AssertionError(msg)
AssertionError: 
Arrays are not equal

x and y nan location mismatch:
 x: array([ nan+infj])
 y: array(infj)

----------------------------------------------------------------------
Ran 3533 tests in 14.446s

FAILED (KNOWNFAIL=3, SKIP=1, failures=8)
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

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM', None, 0.5, <function
aslinearoperator at 0x107f97398>, None, 'normal')
----------------------------------------------------------------------
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/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  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=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=normal
(mismatch 100.0%)
 x: array([[ 0.23815642,  0.1763755 ],
       [-0.10785346, -0.32103487],
       [ 0.12468303, -0.11230416],...
 y: array([[ 0.23815642,  0.24814051],
       [-0.10785347, -0.15634772],
       [ 0.12468302,  0.05671416],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM', None, 0.5, <function
aslinearoperator at 0x107f97398>, None, 'cayley')
----------------------------------------------------------------------
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/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  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=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=cayley
(mismatch 100.0%)
 x: array([[ 0.23815693, -0.33630507],
       [-0.10785286,  0.02168   ],
       [ 0.12468344, -0.11036437],...
 y: array([[ 0.23815643, -0.2405392 ],
       [-0.10785349,  0.14390968],
       [ 0.12468311, -0.04574991],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LA', None, 0.5, <function
aslinearoperator at 0x107f97398>, None, 'normal')
----------------------------------------------------------------------
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/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  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=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=normal
(mismatch 100.0%)
 x: array([[  28.80129188,   -0.6379945 ],
       [  34.79312355,    0.27066791],
       [-270.23255444,    0.4851834 ],...
 y: array([[  3.93467650e+03,  -6.37994494e-01],
       [  3.90913859e+03,   2.70667916e-01],
       [ -3.62176382e+04,   4.85183382e-01],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'SA', None, 0.5, <function
aslinearoperator at 0x107f97398>, None, 'normal')
----------------------------------------------------------------------
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/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  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=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=SA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=normal
(mismatch 100.0%)
 x: array([[ 0.26260981,  0.23815559],
       [-0.09760907, -0.10785484],
       [ 0.06149647,  0.12468203],...
 y: array([[ 0.23744165,  0.2381564 ],
       [-0.13633069, -0.10785359],
       [ 0.03132561,  0.12468301],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'SA', None, 0.5, <function
aslinearoperator at 0x107f97398>, None, 'cayley')
----------------------------------------------------------------------
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/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  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=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=SA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=cayley
(mismatch 100.0%)
 x: array([[ 0.29524244, -0.2381569 ],
       [-0.08169955,  0.10785299],
       [ 0.06645597, -0.12468332],...
 y: array([[ 0.24180251, -0.23815646],
       [-0.14191195,  0.10785349],
       [ 0.03568392, -0.12468307],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <gen-symmetric>, 'f', 2, 'SM', None, 0.5, <function
aslinearoperator at 0x107f97398>, None, 'buckling')
----------------------------------------------------------------------
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/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  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=0.00178814, atol=0.000357628
error for eigsh:general, typ=f, which=SM, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=buckling
(mismatch 100.0%)
 x: array([[-0.10940548,  0.01676016],
       [-0.07154097,  0.4628113 ],
       [ 0.06895222,  0.49206394],...
 y: array([[-0.10940547,  0.05459438],
       [-0.07154103,  0.31407543],
       [ 0.06895217,  0.37578294],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <gen-symmetric>, 'f', 2, 'SA', None, 0.5, <function
aslinearoperator at 0x107f97398>, None, 'cayley')
----------------------------------------------------------------------
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/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 235, in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
  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=0.00178814, atol=0.000357628
error for eigsh:general, typ=f, which=SA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=cayley
(mismatch 100.0%)
 x: array([[-0.4404992 , -0.01935683],
       [-0.25650678, -0.11053132],
       [-0.36893024, -0.13223556],...
 y: array([[-0.44017013, -0.0193569 ],
       [-0.25525379, -0.11053158],
       [-0.36818443, -0.13223571],...

----------------------------------------------------------------------
Ran 5101 tests in 51.423s

FAILED (KNOWNFAIL=12, SKIP=42, failures=16)

Hi,

13.02.2012 17:58, Paul Anton Letnes kirjoitti:
> 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.

The Arpack-related failures you see this time are precision errors, due
to doing iterative inverses within an iterative eigenvalue problem
solution.

So, it's more of a problem with the tests than with ARPACK. If you can
check that the following silences them, it would be appreciated:

    https://github.com/pv/scipy-work/tree/bug/arpack-tol-0101

--

-- 
Pauli Virtanen

On 14.02.2012, at 21:19, Pauli Virtanen wrote:
> The Arpack-related failures you see this time are precision errors, due
> to doing iterative inverses within an iterative eigenvalue problem
> solution.
> 
> So, it's more of a problem with the tests than with ARPACK. If you can
> check that the following silences them, it would be appreciated:
> 
>    https://github.com/pv/scipy-work/tree/bug/arpack-tol-0101
> 

I just tested your arpack-tol-0101 branch and indeed scipy.test() does not show any failures nor errors
with your changes.
The "official 0.10.1rc" still has these (8, I think) arpack failues.

_______________________________________________
SciPy-Dev mailing list
SciPy-Dev <at> scipy.org
http://mail.scipy.org/mailman/listinfo/scipy-dev

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` a
 re 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

> 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

After rebuilding with the recommended gfortran-4.2 this is the output from the tests. It does look better
now. Let me know if you want me to try something else (like verbose=2). Oh, and by the way - this is 0.10.rc2.

Cheers
Paul

Tests:

(scipy-test)i-courant ~/Downloads % python -c 'import scipy;scipy.test(verbose=1)'
Running unit tests for scipy
NumPy version 1.6.1
NumPy is installed in /usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy
SciPy version 0.10.1rc2
SciPy is installed in /Users/paulanto/Downloads/scipy-0.10.1rc2/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/Downloads/scipy-0.10.1rc2/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/Downloads/scipy-0.10.1rc2/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....../usr/local/Cellar/python/2.7.2/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)))
............................................................................................................................................................................................................................................................................................................................................................................................................................................./Users/paulanto/Downloads/scipy-0.10.1rc2/scipy-test/lib/python2.7/site-packages/scipy/io/wavfile.py:31:
WavFileWarning: Unfamiliar format bytes
  warnings.warn("Unfamiliar format bytes",
WavFileWarning)
/Users/paulanto/Downloads/scipy-0.10.1rc2/scipy-test/lib/python2.7/site-packages/scipy/io/wavfile.py:121:
WavFileWarning: chunk not understood
  warnings.warn("chunk not understood", WavFileWarning)
...............................................................................................................................................................................................................................SSSSSS......SSSSSS......SSSS...............................................................................S............................................................................................................................................................................................................................................................K......................................................................................................................................................................................................SSSSS............S
 ..............................................................................................................................................................................................

............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSSSSSSS.........../Users/paulanto/Downloads/scipy-0.10.1rc2/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` "
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
 ............................................................K...............................................................K.................................................................
 ..........................................................................................KK.............................................................................................................................................................................................................................................................................................................................................................................................................................................K.K...................................................................................................................................................................................................................................................................................
 ..........................................................................................................K........K..............SSSSSSS.....................................................
 .....................................................................................................S..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 5101 tests in 53.247s

OK (KNOWNFAIL=12, SKIP=42)

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On 11 February 2012 16:11, Ralf Gommers <ralf.gommers <at> googlemail.com> wrote:
> I am pleased to announce the availability of the first release candidate of
> SciPy 0.10.1. Please try out this release and report any problems on the
> scipy-dev mailing list. If no problems are found, the final release will be
> available in one week.

I just noticed that building with Bento doesn't work from a source
distribution. There's a pull request that fixes this at
https://github.com/scipy/scipy/pull/158.

Since the 0.10.0 release notes advertise Bento build support I wonder
whether this commit
https://github.com/scipy/scipy/commit/6907a2bffb1484623de3afe130e1a13804dec1b1
and the pull request mentioned above (or similar fix) should both be
included in the 0.10.1 release?

Cheers,
Scott

On 14 February 2012 14:22, Scott Sinclair <scott.sinclair.za <at> gmail.com> wrote:
> On 11 February 2012 16:11, Ralf Gommers <ralf.gommers <at> googlemail.com> wrote:
>> I am pleased to announce the availability of the first release candidate of
>> SciPy 0.10.1. Please try out this release and report any problems on the
>> scipy-dev mailing list. If no problems are found, the final release will be
>> available in one week.
>
> I just noticed that building with Bento doesn't work from a source
> distribution. There's a pull request that fixes this at
> https://github.com/scipy/scipy/pull/158.
>
> Since the 0.10.0 release notes advertise Bento build support I wonder
> whether this commit
> https://github.com/scipy/scipy/commit/6907a2bffb1484623de3afe130e1a13804dec1b1
> and the pull request mentioned above (or similar fix) should both be
> included in the 0.10.1 release?

Hmmm - https://github.com/scipy/scipy/commit/6907a2bffb1484623de3afe130e1a13804dec1b1
isn't actually necessary for 0.10.x, but
https://github.com/scipy/scipy/pull/158 is.

Cheers,
Scott

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