Issue 1:
I ran into this problem several times already with different installation methods. This time i used brew to install scipy:

brew tap homebrew/science
brew tap samueljohn/python
brew update
brew install python
pip install nose
brew install scipy

If you then run the tests the following errors occur: https://gist.github.com/joernhees/5733199

A shortened version here:

$ ipython
Python 2.7.5 (default, Jun 8 2013, 00:27:06)
Type "copyright", "credits" or "license" for more information.

IPython 0.13.2 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object', use 'object??' for extra details.

In [1]: import scipy

In [2]: scipy.test()
Running unit tests for scipy
NumPy version 1.7.1
NumPy is installed in /usr/local/lib/python2.7/site-packages/numpy
SciPy version 0.12.0
SciPy is installed in /usr/local/lib/python2.7/site-packages/scipy
Python version 2.7.5 (default, Jun 8 2013, 00:27:06) [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)]
nose version 1.3.0
/usr/local/lib/python2.7/site-packages/numpy/lib/utils.py:139: DeprecationWarning: `scipy.lib.blas` is deprecated, use `scipy.linalg.blas` instead!
warnings.warn(depdoc, DeprecationWarning)
/usr/local/lib/python2.7/site-packages/numpy/lib/utils.py:139: DeprecationWarning: `scipy.lib.lapack` is deprecated, use `scipy.linalg.lapack` instead!
warnings.warn(depdoc, DeprecationWarning)
...............................................K...............................................K..K........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSS......SSSSSS......S..........K..............................................................................................................................................................................................................................................................................................K...................................................................................................................................................................................................../usr/local/lib/python2.7/site-packages/scipy/misc/pilutil.py:230: DeprecationWarning: fromstring() is deprecated. Please call frombytes() instead.
image = Image.fromstring('L',shape,bytedata.tostring())
/usr/local/lib/python2.7/site-packages/scipy/misc/pilutil.py:230: DeprecationWarning: fromstring() is deprecated. Please call frombytes() instead.
image = Image.fromstring('L',shape,bytedata.tostring())
/usr/local/lib/python2.7/site-packages/scipy/misc/pilutil.py:230: DeprecationWarning: fromstring() is deprecated. Please call frombytes() instead.
image = Image.fromstring('L',shape,bytedata.tostring())
/usr/local/lib/python2.7/site-packages/scipy/misc/pilutil.py:230: DeprecationWarning: fromstring() is deprecated. Please call frombytes() instead.
image = Image.fromstring('L',shape,bytedata.tostring())
/usr/local/lib/python2.7/site-packages/scipy/misc/pilutil.py:230: DeprecationWarning: fromstring() is deprecated. Please call frombytes() instead.
image = Image.fromstring('L',shape,bytedata.tostring())
./usr/local/lib/python2.7/site-packages/scipy/misc/pilutil.py:230: DeprecationWarning: fromstring() is deprecated. Please call frombytes() instead.
image = Image.fromstring('L',shape,bytedata.tostring())
./usr/local/lib/python2.7/site-packages/scipy/misc/pilutil.py:230: DeprecationWarning: fromstring() is deprecated. Please call frombytes() instead.
image = Image.fromstring('L',shape,bytedata.tostring())
.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FFF.....FFF..FF......FF..F..........FFF.....FFF..............FF..FF.FFF..FF..FF..FF..F..........FF..FFF.FFF.............F.......F....F.......F..............FFF......FF.............F...F...F....F...F...F..............FFF.FFF.FFF..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K....................................................................K......................................................................................................................................................................KK.................................................................................................................................................................................................................................................................................................................................................................................................................................K........K.......................................................................................................................................................................................................................S...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM', None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 259, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/usr/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 1179, in assert_allclose
verbose=verbose, header=header)
File "/usr/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 645, 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=csr_matrix, OPpart=None, mode=normal
(mismatch 100.0%)
x: array([[ 2.38156418e-01, -6.75444982e+09],
[ -1.07853470e-01, -8.01245676e+09],
[ 1.24683023e-01, -5.19757686e+09],...
y: array([[ 2.38156418e-01, -5.70949789e+08],
[ -1.07853470e-01, -4.05829392e+08],
[ 1.24683023e-01, 6.25800146e+07],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM', None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'buckling')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 259, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/usr/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 1179, in assert_allclose
verbose=verbose, header=header)
File "/usr/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 645, 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=csr_matrix, OPpart=None, mode=buckling
(mismatch 100.0%)
x: array([[ 3.53755447e-01, -2.29114355e+04],
[ -1.60204595e-01, -6.65625445e+04],
[ 1.85203065e-01, -2.69012500e+04],...
y: array([[ 3.53755447e-01, -8.88255444e+05],
[ -1.60204595e-01, -2.39343354e+06],
[ 1.85203065e-01, -3.96842525e+04],...

======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM', None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 259, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/usr/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 1179, in assert_allclose
verbose=verbose, header=header)
File "/usr/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 645, 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=csr_matrix, OPpart=None, mode=cayley
(mismatch 100.0%)
x: array([[ -2.38156418e-01, 1.04661597e+09],
[ 1.07853470e-01, 1.39930271e+09],
[ -1.24683023e-01, 9.56906461e+08],...
y: array([[ -2.38156418e-01, 7.63721281e+07],
[ 1.07853470e-01, 1.25169905e+08],
[ -1.24683023e-01, 2.91283130e+07],...

======================================================================
...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <gen-symmetric>, 'd', 2, 'SA', None, 0.5, <function asarray at 0x10ad03e60>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 259, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/usr/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 1179, in assert_allclose
verbose=verbose, header=header)
File "/usr/local/lib/python2.7/site-packages/numpy/testing/utils.py", line 645, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=4.44089e-13, atol=4.44089e-13
error for eigsh:general, typ=d, which=SA, sigma=0.5, mattype=asarray, OPpart=None, mode=cayley
(mismatch 100.0%)
x: array([[-0.36892684, -0.01935691],
[-0.26850996, -0.11053158],
[-0.40976156, -0.13223572],...
y: array([[-0.43633077, -0.01935691],
[-0.25161386, -0.11053158],
[-0.36756684, -0.13223572],...

----------------------------------------------------------------------
Ran 4831 tests in 54.169s

FAILED (KNOWNFAIL=11, SKIP=14, failures=63)
Out[2]: <nose.result.TextTestResult run=4831 errors=0 failures=63>

In [3]:

Issue 2:
Original ticket http://projects.scipy.org/scipy/ticket/1853 on 2013-02-26 by @zyv, assigned to trac user jakevdp.

Hi,

I've just upgraded to the latest NumPy / SciPy avaiable via pip and am seeing lots of test failures in SciPy, even though the test suite of NumPy Passes without any problems.

I'm running Ubuntu 10.10 and Python 2.7.1 from ActiveState on a x86_64 i5 CPU.

My configuration is as follows:

$ python -c 'import numpy.distutils.__config__ as npc; npc.show()'
atlas_threads_info:
libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/usr/lib/atlas-corei7sse3/atlas', '/usr/lib/atlas-corei7sse3']
define_macros = [('NO_ATLAS_INFO', -1)]
language = f77
include_dirs = ['/usr/include/atlas']
blas_opt_info:
libraries = ['ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/usr/lib/atlas-corei7sse3']
define_macros = [('NO_ATLAS_INFO', -1)]
language = c
include_dirs = ['/usr/include/atlas']
atlas_blas_threads_info:
libraries = ['ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/usr/lib/atlas-corei7sse3']
define_macros = [('NO_ATLAS_INFO', -1)]
language = c
include_dirs = ['/usr/include/atlas']
lapack_opt_info:
libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/usr/lib/atlas-corei7sse3/atlas', '/usr/lib/atlas-corei7sse3']
define_macros = [('NO_ATLAS_INFO', -1)]
language = f77
include_dirs = ['/usr/include/atlas']
lapack_mkl_info:
NOT AVAILABLE
blas_mkl_info:
NOT AVAILABLE
mkl_info:
NOT AVAILABLE

Please let me know if I can provide any additional useful information.