Python 使用pip/virtualenv和XCode 4.6.3在MacOS Mountain Lion上的SciPy测试失败

我在运行一个名为nsilk的质谱代码时遇到了一个问题，它依赖于NumPy、SciPy和BioPython。因为我在Mac（Mountain Lion）上运行了其他基于Python的项目，所以我想使用virtualenv/pip分离虚拟环境，以便安装nsilk

运行nsilk命令后（我已使用“which”检查它是否指向驻留在虚拟环境中的版本，而不是系统范围的安装），我收到以下回溯：

Traceback (most recent call last):
  File "/usr/local/bin/nsilk", line 32, in <module>
    import xllib
  File "/Library/Python/2.7/site-packages/xllib/__init__.py", line 30, in <module>
    import MSMS
  File "/Library/Python/2.7/site-packages/xllib/MSMS.py", line 32, in <module>
    import scipy.stats as ss
ImportError: No module named scipy.stats

但是，当我运行scipy.test（）时，会收到大量错误：

>>> import scipy
>>> scipy.test()

以下是前三项：

======================================================================
ERROR: test_logm_consistency (test_matfuncs.TestExpM)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/sparse/linalg/tests/test_matfuncs.py", line 55, in test_logm_consistency
    assert_array_almost_equal(expm(logm(a)), a)
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/linalg/matfuncs.py", line 387, in logm
    errest = norm(expm(F)-A,1) / norm(A,1)
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/linalg/matfuncs.py", line 55, in expm
    return scipy.sparse.linalg.expm(A)
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/sparse/linalg/matfuncs.py", line 85, in expm
    A_L1 = norm(A,1)
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/linalg/misc.py", line 116, in norm
    a = np.asarray_chkfinite(a)
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/numpy/lib/function_base.py", line 590, in asarray_chkfinite
    "array must not contain infs or NaNs")
ValueError: array must not contain infs or NaNs

======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 62, in test_asum
    assert_almost_equal(f([3,-4,5]),12)
  File "/Users/Mike/venvs/nsilk/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/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 71, in test_dot
    assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
  File "/Users/Mike/venvs/nsilk/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

我使用pip安装了NumPy、SciPy和BioPython，在安装了XCode 4.6.3之后，使用GCC 4.8.0 20120603（实验版）。我最初在安装SciPy时遇到了麻烦，因为它缺少一个名为LibFFTPack（或类似）的库而失败

谷歌搜索错误导致需要为XCode安装Fortran编译器。这“修复”了在执行pip时对SciPy编译的那些回溯，但导致了上述问题！我猜想是由于某些编译错误导致了SciPy的错误安装。这里可能存在编译器/二进制混合问题吗

干杯，迈克

======================================================================
ERROR: test_logm_consistency (test_matfuncs.TestExpM)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/sparse/linalg/tests/test_matfuncs.py", line 55, in test_logm_consistency
    assert_array_almost_equal(expm(logm(a)), a)
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/linalg/matfuncs.py", line 387, in logm
    errest = norm(expm(F)-A,1) / norm(A,1)
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/linalg/matfuncs.py", line 55, in expm
    return scipy.sparse.linalg.expm(A)
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/sparse/linalg/matfuncs.py", line 85, in expm
    A_L1 = norm(A,1)
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/linalg/misc.py", line 116, in norm
    a = np.asarray_chkfinite(a)
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/numpy/lib/function_base.py", line 590, in asarray_chkfinite
    "array must not contain infs or NaNs")
ValueError: array must not contain infs or NaNs

======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 62, in test_asum
    assert_almost_equal(f([3,-4,5]),12)
  File "/Users/Mike/venvs/nsilk/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/Mike/venvs/nsilk/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 71, in test_dot
    assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
  File "/Users/Mike/venvs/nsilk/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