[Debian-med-packaging] Bug#906156: python-skbio ftbfs in unstable, and autopkg tests fail (Python 3.7 tests)
Matthias Klose
doko at debian.org
Wed Aug 15 08:03:41 BST 2018
Package: src:python-skbio
Version: 0.5.2-1
Severity: serious
Tags: sid buster
python-skbio ftbfs in unstable (Python 3.7 tests)
https://ci.debian.net/data/packages/unstable/amd64/p/python-skbio/latest-autopkgtest/log.gz
======================================================================
ERROR: test_bool_index_both_axes (skbio.alignment.tests.test_tabular_msa.TestLoc)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1091, in test_bool_index_both_axes
new = self.get(msa, ([False, True, True], [True, True, False]))
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1271, in get
return obj.loc[indexable]
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 38, in __getitem__
return self._handle_both_axes(*indexable)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 52, in _handle_both_axes
r = self._slice_on_first_axis(self._obj, seq_index)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 71, in _slice_on_first_axis
if self.is_scalar(indexable, axis=0):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 171, in is_scalar
duplicated_key = indexable in index.get_duplicates()
File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 2035,
in __contains__
hash(key)
TypeError: unhashable type: 'list'
======================================================================
ERROR: test_bool_index_first_axis (skbio.alignment.tests.test_tabular_msa.TestLoc)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1062, in test_bool_index_first_axis
new = self.get(msa, [True, True, False])
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1271, in get
return obj.loc[indexable]
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 42, in __getitem__
return self._slice_on_first_axis(self._obj, indexable)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 71, in _slice_on_first_axis
if self.is_scalar(indexable, axis=0):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 171, in is_scalar
duplicated_key = indexable in index.get_duplicates()
File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 2035,
in __contains__
hash(key)
TypeError: unhashable type: 'list'
======================================================================
ERROR: test_bool_index_second_axis (skbio.alignment.tests.test_tabular_msa.TestLoc)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1076, in test_bool_index_second_axis
new = self.get(msa, (Ellipsis, [True, True, False]))
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1271, in get
return obj.loc[indexable]
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 38, in __getitem__
return self._handle_both_axes(*indexable)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 50, in _handle_both_axes
return self._slice_on_second_axis(self._obj, pos_index)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 62, in _slice_on_second_axis
if self.is_scalar(indexable, axis=1):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 171, in is_scalar
duplicated_key = indexable in index.get_duplicates()
File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 2035,
in __contains__
hash(key)
TypeError: unhashable type: 'list'
======================================================================
ERROR: test_bool_index_too_big (skbio.alignment.tests.test_tabular_msa.TestLoc)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1103, in test_bool_index_too_big
self.get(msa, [False, False, False, False])
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1271, in get
return obj.loc[indexable]
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 42, in __getitem__
return self._slice_on_first_axis(self._obj, indexable)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 71, in _slice_on_first_axis
if self.is_scalar(indexable, axis=0):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 171, in is_scalar
duplicated_key = indexable in index.get_duplicates()
File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 2035,
in __contains__
hash(key)
TypeError: unhashable type: 'list'
======================================================================
ERROR: test_bool_index_too_small (skbio.alignment.tests.test_tabular_msa.TestLoc)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1119, in test_bool_index_too_small
self.get(msa, [False])
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1271, in get
return obj.loc[indexable]
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 42, in __getitem__
return self._slice_on_first_axis(self._obj, indexable)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 71, in _slice_on_first_axis
if self.is_scalar(indexable, axis=0):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 171, in is_scalar
duplicated_key = indexable in index.get_duplicates()
File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 2035,
in __contains__
hash(key)
TypeError: unhashable type: 'list'
======================================================================
ERROR: test_unhashable_index_both_axes
(skbio.alignment.tests.test_tabular_msa.TestLoc)
----------------------------------------------------------------------
TypeError: unhashable type: 'list'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1461, in test_unhashable_index_both_axes
self.get(msa, (s, 0))
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1271, in get
return obj.loc[indexable]
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 38, in __getitem__
return self._handle_both_axes(*indexable)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 52, in _handle_both_axes
r = self._slice_on_first_axis(self._obj, seq_index)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 71, in _slice_on_first_axis
if self.is_scalar(indexable, axis=0):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 171, in is_scalar
duplicated_key = indexable in index.get_duplicates()
File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 1926,
in get_duplicates
return self[self.duplicated()].unique()
File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 4539,
in duplicated
return super(Index, self).duplicated(keep=keep)
File "/usr/lib/python3/dist-packages/pandas/core/base.py", line 1250, in
duplicated
return duplicated(self, keep=keep)
File "/usr/lib/python3/dist-packages/pandas/core/algorithms.py", line 798, in
duplicated
return f(values, keep=keep)
SystemError: <built-in function duplicated_object> returned a result with an
error set
======================================================================
ERROR: test_unhashable_index_first_axis
(skbio.alignment.tests.test_tabular_msa.TestLoc)
----------------------------------------------------------------------
TypeError: unhashable type: 'slice'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1433, in test_unhashable_index_first_axis
self.get(msa, s, axis=0)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1273, in get
return obj.loc(axis=axis)[indexable]
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 29, in __getitem__
return self._slice_on_first_axis(self._obj, indexable)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 71, in _slice_on_first_axis
if self.is_scalar(indexable, axis=0):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 171, in is_scalar
duplicated_key = indexable in index.get_duplicates()
File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 1926,
in get_duplicates
return self[self.duplicated()].unique()
File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 4539,
in duplicated
return super(Index, self).duplicated(keep=keep)
File "/usr/lib/python3/dist-packages/pandas/core/base.py", line 1250, in
duplicated
return duplicated(self, keep=keep)
File "/usr/lib/python3/dist-packages/pandas/core/algorithms.py", line 798, in
duplicated
return f(values, keep=keep)
SystemError: <built-in function duplicated_object> returned a result with an
error set
======================================================================
ERROR: test_unhashable_index_second_axis
(skbio.alignment.tests.test_tabular_msa.TestLoc)
----------------------------------------------------------------------
TypeError: unhashable type: 'slice'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1446, in test_unhashable_index_second_axis
self.get(msa, [0, 1], axis=1)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 1273, in get
return obj.loc(axis=axis)[indexable]
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 31, in __getitem__
return self._slice_on_second_axis(self._obj, indexable)
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 62, in _slice_on_second_axis
if self.is_scalar(indexable, axis=1):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/_indexing.py",
line 171, in is_scalar
duplicated_key = indexable in index.get_duplicates()
File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 1926,
in get_duplicates
return self[self.duplicated()].unique()
File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 4539,
in duplicated
return super(Index, self).duplicated(keep=keep)
File "/usr/lib/python3/dist-packages/pandas/core/base.py", line 1250, in
duplicated
return duplicated(self, keep=keep)
File "/usr/lib/python3/dist-packages/pandas/core/algorithms.py", line 798, in
duplicated
return f(values, keep=keep)
SystemError: <built-in function duplicated_object> returned a result with an
error set
======================================================================
FAIL: test_with_positional_metadata
(skbio.alignment.tests.test_tabular_msa.TestIterPositions)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 2958, in test_with_positional_metadata
'bar': [np.nan, np.nan, 'bazz']})])
AssertionError: Lists differ: [Sequ[50 chars]o': 9.0
'pm1': 0.5
Positional metadata:
[313 chars] C--] != [Sequ[50 chars]o': 9
'pm1': 0.5
Positional metadata:
[309 chars] C--]
First differing element 0:
Seque[49 chars]o': 9.0
'pm1': 0.5
Positional metadata:
[102 chars]0 AA-
Seque[49 chars]o': 9
'pm1': 0.5
Positional metadata:
[100 chars]0 AA-
[Sequence
---------------------------
Metadata:
- 'foo': 9.0
? --
+ 'foo': 9
'pm1': 0.5
Positional metadata:
+ 'foo': <dtype: float64>
'bar': <dtype: object>
- 'foo': <dtype: float64>
Stats:
length: 3
---------------------------
0 AA-,
Sequence
---------------------------
Metadata:
- 'foo': 99.0
? --
+ 'foo': 99
'pm1': 1.5
Positional metadata:
+ 'foo': <dtype: float64>
'bar': <dtype: object>
- 'foo': <dtype: float64>
Stats:
length: 3
---------------------------
0 C--]
======================================================================
FAIL: test_with_positional_metadata_reverse
(skbio.alignment.tests.test_tabular_msa.TestIterPositions)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 2979, in test_with_positional_metadata_reverse
'bar': [np.nan, np.nan, 'baz']})])
AssertionError: Lists differ: [Sequ[51 chars]': 99.0
'pm1': 1.5
Positional metadata:
[312 chars] AA-] != [Sequ[51 chars]': 99
'pm1': 1.5
Positional metadata:
[308 chars] AA-]
First differing element 0:
Seque[50 chars]': 99.0
'pm1': 1.5
Positional metadata:
[102 chars]0 C--
Seque[50 chars]': 99
'pm1': 1.5
Positional metadata:
[100 chars]0 C--
[Sequence
---------------------------
Metadata:
- 'foo': 99.0
? --
+ 'foo': 99
'pm1': 1.5
Positional metadata:
+ 'foo': <dtype: float64>
'bar': <dtype: object>
- 'foo': <dtype: float64>
Stats:
length: 3
---------------------------
0 C--,
Sequence
---------------------------
Metadata:
- 'foo': 9.0
? --
+ 'foo': 9
'pm1': 0.5
Positional metadata:
+ 'foo': <dtype: float64>
'bar': <dtype: object>
- 'foo': <dtype: float64>
Stats:
length: 3
---------------------------
0 AA-]
======================================================================
FAIL: test_how_outer (skbio.alignment.tests.test_tabular_msa.TestJoin)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 2770, in test_how_outer
'baz': [np.nan, np.nan, 'c', 'd', 'e']}))
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/alignment/tests/test_tabular_msa.py",
line 2521, in assertEqualJoinedMSA
self.assertEqual(msa1, msa2)
AssertionError: Tabul[59 chars] 'bar': <dtype: object>
'baz': <dtype: [136 chars]----- != Tabul[59 chars] 'foo': <dtype: int64>
'bar': <dtype: o[136 chars]-----
======================================================================
FAIL: test_not_equal (skbio.util.tests.test_testing.TestAssertDataFrameAlmostEqual)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_skbio/build/skbio/util/tests/test_testing.py",
line 211, in test_not_equal
assert_data_frame_almost_equal(df1, df2)
AssertionError: AssertionError not raised
----------------------------------------------------------------------
Ran 2314 tests in 70.280s
FAILED (SKIP=30, errors=8, failures=4)
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