在 Mac 上安装了 scikit-bio,并安装了 scikit-bio 的依赖项。收到以下错误。包括追溯。按照https://pypi.python.org/pypi/scikit-bio上的说明进行 skbio 测试并使用“conda install scikit-bio”安装,没有错误或问题。
有人可以帮助我了解我在哪里遇到问题吗?谢谢
TT0463-5:~ ron$ nosetests --with-doctest skbio
............................................................................./Users/ron/anaconda/lib/python2.7/site-packages/skbio/alignment/_pairwise.py:594: UserWarning: make_identity_substitution_matrix is deprecated and will soon be replaced, though at the time of this writing the new name has not been finalized. Updates will be posted to issue #161: https://github.com/biocore/scikit-bio/issues/161
warn("make_identity_substitution_matrix is deprecated and will soon be "
.............................................................................................../Users/ron/anaconda/lib/python2.7/site-packages/numpy/core/_methods.py:59: RuntimeWarning: Mean of empty slice.
warnings.warn("Mean of empty slice.", RuntimeWarning)
EEE..........................F...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
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ERROR: Test correctly handles coloring of box plots.
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Traceback (most recent call last):
File "/Users/ron/anaconda/lib/python2.7/site-packages/skbio/draw/tests/test_distributions.py", line 492, in test_boxplots_box_colors
fig = boxplots([[], [], []], box_colors=['blue', 'red', 'yellow'])
File "/Users/ron/anaconda/lib/python2.7/site-packages/skbio/draw/_distributions.py", line 125, in boxplots
whis=whisker_length, widths=box_width)
File "/Users/ron/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py", line 2636, in boxplot
meanprops=meanprops, manage_xticks=manage_xticks)
File "/Users/ron/anaconda/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 3045, in boxplot
labels=labels)
File "/Users/ron/anaconda/lib/python2.7/site-packages/matplotlib/cbook.py", line 1965, in boxplot_stats
q1, med, q3 = np.percentile(x, [25, 50, 75])
File "/Users/ron/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py", line 3042, in percentile
interpolation=interpolation)
File "/Users/ron/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py", line 2791, in _ureduce
r = func(a, **kwargs)
File "/Users/ron/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py", line 3131, in _percentile
x1 = take(ap, indices_below, axis=axis) * weights_below
File "/Users/ron/anaconda/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 121, in take
return take(indices, axis, out, mode)
IndexError: cannot do a non-empty take from an empty axes.
======================================================================
ERROR: Test functions correctly with empty distributions.
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Traceback (most recent call last):
File "/Users/ron/anaconda/lib/python2.7/site-packages/skbio/draw/tests/test_distributions.py", line 470, in test_boxplots_empty_distributions
"y-axis label")
File "/Users/ron/anaconda/lib/python2.7/site-packages/skbio/draw/_distributions.py", line 125, in boxplots
whis=whisker_length, widths=box_width)
File "/Users/ron/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py", line 2636, in boxplot
meanprops=meanprops, manage_xticks=manage_xticks)
File "/Users/ron/anaconda/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 3045, in boxplot
labels=labels)
File "/Users/ron/anaconda/lib/python2.7/site-packages/matplotlib/cbook.py", line 1965, in boxplot_stats
q1, med, q3 = np.percentile(x, [25, 50, 75])
File "/Users/ron/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py", line 3042, in percentile
interpolation=interpolation)
File "/Users/ron/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py", line 2791, in _ureduce
r = func(a, **kwargs)
File "/Users/ron/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py", line 3131, in _percentile
x1 = take(ap, indices_below, axis=axis) * weights_below
File "/Users/ron/anaconda/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 121, in take
return take(indices, axis, out, mode)
IndexError: cannot do a non-empty take from an empty axes.
======================================================================
ERROR: Test correctly throws error on invalid input.
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Traceback (most recent call last):
File "/Users/ron/anaconda/lib/python2.7/site-packages/skbio/draw/tests/test_distributions.py", line 514, in test_boxplots_invalid_input
boxplots([[1, 2, 3], [], [4, 5, 6]], box_colors=['blue', 'red'])
File "/Users/ron/anaconda/lib/python2.7/site-packages/skbio/draw/_distributions.py", line 125, in boxplots
whis=whisker_length, widths=box_width)
File "/Users/ron/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py", line 2636, in boxplot
meanprops=meanprops, manage_xticks=manage_xticks)
File "/Users/ron/anaconda/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 3045, in boxplot
labels=labels)
File "/Users/ron/anaconda/lib/python2.7/site-packages/matplotlib/cbook.py", line 1965, in boxplot_stats
q1, med, q3 = np.percentile(x, [25, 50, 75])
File "/Users/ron/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py", line 3042, in percentile
interpolation=interpolation)
File "/Users/ron/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py", line 2791, in _ureduce
r = func(a, **kwargs)
File "/Users/ron/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py", line 3131, in _percentile
x1 = take(ap, indices_below, axis=axis) * weights_below
File "/Users/ron/anaconda/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 121, in take
return take(indices, axis, out, mode)
IndexError: cannot do a non-empty take from an empty axes.
======================================================================
FAIL: _plot_box_data() should return a dictionary for Line2D's.
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Traceback (most recent call last):
File "/Users/ron/anaconda/lib/python2.7/site-packages/skbio/draw/tests/test_distributions.py", line 245, in test_plot_box_data
self.assertEqual(len(result['fliers']), 2)
AssertionError: 1 != 2
----------------------------------------------------------------------
Ran 857 tests in 23.956s
FAILED (errors=3, failures=1)