[Debichem-devel] Bug#1071807: prody: FTBFS: ModuleNotFoundError: No module named 'numpy.testing.decorators'
Santiago Vila
sanvila at debian.org
Sat May 25 01:33:24 BST 2024
Package: src:prody
Version: 2.4.1+dfsg-2
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary --buildsystem pybuild --with numpy3,python3
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:311: python3.12 setup.py config
running config
I: pybuild base:311: python3.11 setup.py config
running config
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3.12 setup.py build
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody
[... snipped ...]
testPBCCoordArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testPBCCoordArgumentSwitching) ... ok
testCenter (prody.tests.measure.test_measure.TestCenter.testCenter) ... ok
testCenterWithWeights (prody.tests.measure.test_measure.TestCenter.testCenterWithWeights) ... ok
testMultiCoordsets (prody.tests.measure.test_measure.TestCenter.testMultiCoordsets) ... ok
testMultiCoordsetsWithWeights (prody.tests.measure.test_measure.TestCenter.testMultiCoordsetsWithWeights) ... ok
testCTerPhi (prody.tests.measure.test_measure.TestDihedrals.testCTerPhi) ... ok
testCTerPsi (prody.tests.measure.test_measure.TestDihedrals.testCTerPsi) ... ok
testCalcPhi (prody.tests.measure.test_measure.TestDihedrals.testCalcPhi) ... ok
testCalcPsi (prody.tests.measure.test_measure.TestDihedrals.testCalcPsi) ... ok
testNTerPhi (prody.tests.measure.test_measure.TestDihedrals.testNTerPhi) ... ok
testNTerPsi (prody.tests.measure.test_measure.TestDihedrals.testNTerPsi) ... ok
testPBC (prody.tests.measure.test_measure.TestDistances.testPBC) ... ok
testPBCSymmetry (prody.tests.measure.test_measure.TestDistances.testPBCSymmetry) ... ok
testMSF (prody.tests.measure.test_measure.TestMSF.testMSF) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory/dcdfile.py:273: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
xyz = fromstring(self._file.read(self._itemsize * n_floats),
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory/dcdfile.py:320: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
data = fromstring(data, self._dtype)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/trajectory/dcdfile.py:294: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
unitcell = fromstring(self._file.read(48), dtype=np.float64)
ok
testMSFfloat (prody.tests.measure.test_measure.TestMSF.testMSFfloat) ... ok
testByArgument (prody.tests.measure.test_transform.TestMoveAtoms.testByArgument) ... ok
testToArgument (prody.tests.measure.test_transform.TestMoveAtoms.testToArgument) ... ok
testTransformation (prody.tests.measure.test_transform.TestMoveAtoms.testTransformation) ... ok
testWrap (prody.tests.measure.test_transform.TestWrapAtoms.testWrap) ... ok
prody.tests.proteins.test_ciffile (unittest.loader._FailedTest.prody.tests.proteins.test_ciffile) ... ERROR
prody.tests.proteins.test_dssp (unittest.loader._FailedTest.prody.tests.proteins.test_dssp) ... ERROR
testHeaderContent (prody.tests.proteins.test_header.TestParsePDBHeaderOnly.testHeaderContent) ... ok
testHeaderType (prody.tests.proteins.test_header.TestParsePDBHeaderOnly.testHeaderType) ... ok
prody.tests.proteins.test_localpdb (unittest.loader._FailedTest.prody.tests.proteins.test_localpdb) ... ERROR
prody.tests.proteins.test_pdbfile (unittest.loader._FailedTest.prody.tests.proteins.test_pdbfile) ... ERROR
prody.tests.proteins.test_wwpdb (unittest.loader._FailedTest.prody.tests.proteins.test_wwpdb) ... ERROR
testBuildMSAlocal (prody.tests.sequence.test_analysis.TestBuildMSA.testBuildMSAlocal) ... ok
testResidueCount (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testResidueCount) ... ok
testResidueOccupancy (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testResidueOccupancy) ... ok
testSequenceCount (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testSequenceCount) ... ok
testSequenceOccupancy (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testSequenceOccupancy) ... ok
testMATLAB (prody.tests.sequence.test_analysis.TestCalcMeff.testMATLAB) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestCalcMeff.testTwenty) ... ok
testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcMeff.testTwentyReversed) ... ok
testZero1 (prody.tests.sequence.test_analysis.TestCalcMeff.testZero1) ... ok
testZero2 (prody.tests.sequence.test_analysis.TestCalcMeff.testZero2) ... ok
testAmbiguity (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity) ... ok
testAmbiguity2 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity2) ... ok
testAmbiguity3 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity3) ... ok
testAmbiguity4 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity4) ... ok
testAmbiguity5 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity5) ... ok
testAmbiguity6 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity6) ... ok
testAmbiguity7 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity7) ... ok
testInf (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testInf) ... ok
testNoAmbiguity (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNoAmbiguity) ... ok
testNorm (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNorm) ... ok
testNorm2 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNorm2) ... ok
testSixSequences (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testSixSequences) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testTwenty) ... ok
testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testTwentyReversed) ... ok
testAmbiguity (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity) ... ok
testAmbiguity2 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity2) ... ok
testAmbiguity3 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity3) ... ok
testAmbiguity4 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity4) ... ok
testAmbiguity5 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity5) ... ok
testAmbiguity6 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity6) ... ok
testAmbiguity7 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity7) ... ok
testFourSequences (prody.tests.sequence.test_analysis.TestCalcOMES.testFourSequences) ... ok
testInf (prody.tests.sequence.test_analysis.TestCalcOMES.testInf) ... ok
testNoAmbiguity (prody.tests.sequence.test_analysis.TestCalcOMES.testNoAmbiguity) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestCalcOMES.testTwenty) ... ok
testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcOMES.testTwentyReversed) ... ok
testZero (prody.tests.sequence.test_analysis.TestCalcOMES.testZero) ... ok
testMATLAB (prody.tests.sequence.test_analysis.TestCalcSCA.testMATLAB) ... ok
testZero (prody.tests.sequence.test_analysis.TestCalcSCA.testZero) ... ok
testAmbiguous (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testAmbiguous) ... ok
testGapDividend (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testGapDividend) ... ok
testSixSequences (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testSixSequences) ... ok
testSmallProbability (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testSmallProbability) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testTwenty) ... ok
testMATLAB10 (prody.tests.sequence.test_analysis.TestDirectInfo.testMATLAB10) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence/analysis.py:592: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
c = matrix.dot(matrix(zeros((length*q, 1), float)),
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence/analysis.py:593: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
matrix(zeros((1, length*q), float)))
/usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py:70: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
return matrix(data, dtype=dtype, copy=False)
ok
testMATLAB8 (prody.tests.sequence.test_analysis.TestDirectInfo.testMATLAB8) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestDirectInfo.testTwenty) ... ok
testTwentyReversed (prody.tests.sequence.test_analysis.TestDirectInfo.testTwentyReversed) ... ok
testZero (prody.tests.sequence.test_analysis.TestDirectInfo.testZero) ... ok
testZero1 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero1) ... ok
testZero2 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero2) ... ok
testZero3 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero3) ... ok
testZero4 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero4) ... ok
testIdentityMatrix (prody.tests.sequence.test_analysis.TestIdentity.testIdentityMatrix) ... ok
testIdentityMatrixNonTurbo (prody.tests.sequence.test_analysis.TestIdentity.testIdentityMatrixNonTurbo) ... ok
testUnique (prody.tests.sequence.test_analysis.TestUnique.testUnique) ... ok
testUnique2 (prody.tests.sequence.test_analysis.TestUnique.testUnique2) ... ok
testMerge (prody.tests.sequence.test_msa.TestMerging.testMerge) ... ok
testAddition (prody.tests.sequence.test_msa.TestRefinement.testAddition) ... ok
testAll (prody.tests.sequence.test_msa.TestRefinement.testAll) ... ok
testColocc (prody.tests.sequence.test_msa.TestRefinement.testColocc) ... ok
testExtension (prody.tests.sequence.test_msa.TestRefinement.testExtension) ... ok
testLabel (prody.tests.sequence.test_msa.TestRefinement.testLabel) ... ok
testRowCol (prody.tests.sequence.test_msa.TestRefinement.testRowCol) ... ok
testRowocc (prody.tests.sequence.test_msa.TestRefinement.testRowocc) ... ok
testSeqid (prody.tests.sequence.test_msa.TestRefinement.testSeqid) ... ok
testSeqidLabel (prody.tests.sequence.test_msa.TestRefinement.testSeqidLabel) ... ok
prody.tests.sequence.test_msafile (unittest.loader._FailedTest.prody.tests.sequence.test_msafile) ... ERROR
testStringConversion (prody.tests.sequence.test_sequence.TestSequence.testStringConversion) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/sequence/sequence.py:36: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
self._seq = fromstring(args[0], '|S1')
ok
testParseDCD (prody.tests.trajectory.test_dcdfile.TestDCDFile.testParseDCD) ... ok
testWrite (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWrite) ... ok
testWriteDCD (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWriteDCD) ... ok
testWriteModeAppend (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWriteModeAppend) ... ok
testAll (prody.tests.trajectory.test_frame.TestSuperpose.testAll) ... ok
testCarbon (prody.tests.trajectory.test_frame.TestSuperpose.testCarbon) ... ok
testCoords (prody.tests.utilities.test_checkers.TestCheckCoords.testCoords) ... ok
testCoordset (prody.tests.utilities.test_checkers.TestCheckCoords.testCoordset) ... ok
testCoordsetNatoms (prody.tests.utilities.test_checkers.TestCheckCoords.testCoordsetNatoms) ... ok
testInvalidCoords (prody.tests.utilities.test_checkers.TestCheckCoords.testInvalidCoords) ... ok
testCorrectMonotypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMonotypeOneArg) ... ok
testCorrectMonotypeTwoArgs (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMonotypeTwoArgs) ... ok
testCorrectMultitypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMultitypeOneArg) ... ok
testWrongMonotypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMonotypeOneArg) ... ok
testWrongMonotypeTwoArgs (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMonotypeTwoArgs) ... ok
testWrongMultitypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMultitypeOneArg) ... ok
testContinuous (prody.tests.utilities.test_misctools.TestRangeString.testContinuous) ... ok
testGapped (prody.tests.utilities.test_misctools.TestRangeString.testGapped) ... ok
testNegative (prody.tests.utilities.test_misctools.TestRangeString.testNegative) ... ok
testRepeated (prody.tests.utilities.test_misctools.TestRangeString.testRepeated) ... ok
testBuffer (prody.tests.utilities.test_pathtools.TestGunzip.testBuffer) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities/test_pathtools.py:34: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/compressed.txt.gz'>
buff = open(self.gzfn, 'rb').read()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
testFile (prody.tests.utilities.test_pathtools.TestGunzip.testFile) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities/test_pathtools.py:29: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/compressed.txt' mode='r' encoding='UTF-8'>
text = open(fn).read()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
======================================================================
ERROR: prody.tests.apps.test_prody_anm (unittest.loader._FailedTest.prody.tests.apps.test_prody_anm)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_anm
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_anm.py", line 9, in <module>
import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_anm.py", line 11, in <module>
from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
======================================================================
ERROR: prody.tests.apps.test_prody_catdcd (unittest.loader._FailedTest.prody.tests.apps.test_prody_catdcd)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_catdcd
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_catdcd.py", line 8, in <module>
import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_catdcd.py", line 10, in <module>
from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
======================================================================
ERROR: prody.tests.apps.test_prody_examples (unittest.loader._FailedTest.prody.tests.apps.test_prody_examples)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_examples
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_examples.py", line 10, in <module>
import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_examples.py", line 12, in <module>
from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
======================================================================
ERROR: prody.tests.apps.test_prody_gnm (unittest.loader._FailedTest.prody.tests.apps.test_prody_gnm)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_gnm
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_gnm.py", line 8, in <module>
import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_gnm.py", line 10, in <module>
from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
======================================================================
ERROR: prody.tests.apps.test_prody_pca (unittest.loader._FailedTest.prody.tests.apps.test_prody_pca)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_pca
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_pca.py", line 8, in <module>
import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_pca.py", line 10, in <module>
from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
======================================================================
ERROR: prody.tests.atomic.test_select (unittest.loader._FailedTest.prody.tests.atomic.test_select)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.atomic.test_select
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic/test_select.py", line 9, in <module>
import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic/test_select.py", line 11, in <module>
from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
======================================================================
ERROR: prody.tests.dynamics.test_enms (unittest.loader._FailedTest.prody.tests.dynamics.test_enms)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.dynamics.test_enms
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics/test_enms.py", line 7, in <module>
import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics/test_enms.py", line 9, in <module>
from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
======================================================================
ERROR: prody.tests.dynamics.test_pca (unittest.loader._FailedTest.prody.tests.dynamics.test_pca)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.dynamics.test_pca
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics/test_pca.py", line 7, in <module>
import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics/test_pca.py", line 9, in <module>
from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
======================================================================
ERROR: testSelection (prody.tests.ensemble.test_ensemble.TestEnsemble.testSelection)
Test atom selection of ensemble.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble/test_ensemble.py", line 191, in testSelection
sel = ATOMS.select('resnum 1 to 3')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic/atomic.py", line 232, in select
return SELECT.select(self, selstr, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic/select.py", line 895, in select
indices = self.getIndices(atoms, selstr, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic/select.py", line 953, in getIndices
torf = self.getBoolArray(atoms, selstr, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic/select.py", line 1004, in getBoolArray
parser = self._getParser(selstr)
^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/atomic/select.py", line 1103, in _getParser
parser.enablePackrat()
File "/usr/lib/python3/dist-packages/pyparsing/util.py", line 265, in _inner
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pyparsing/core.py", line 1132, in enable_packrat
ParserElement.packrat_cache = _FifoCache(cache_size_limit) # type: ignore[assignment]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pyparsing/util.py", line 105, in __init__
keyring = [object()] * size
~~~~~~~~~~~^~~~~~
TypeError: can't multiply sequence by non-int of type 'Forward'
======================================================================
ERROR: prody.tests.proteins.test_ciffile (unittest.loader._FailedTest.prody.tests.proteins.test_ciffile)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_ciffile
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_ciffile.py", line 8, in <module>
import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_ciffile.py", line 10, in <module>
from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
======================================================================
ERROR: prody.tests.proteins.test_dssp (unittest.loader._FailedTest.prody.tests.proteins.test_dssp)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_dssp
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_dssp.py", line 5, in <module>
import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_dssp.py", line 7, in <module>
from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
======================================================================
ERROR: prody.tests.proteins.test_localpdb (unittest.loader._FailedTest.prody.tests.proteins.test_localpdb)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_localpdb
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_localpdb.py", line 8, in <module>
import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_localpdb.py", line 10, in <module>
from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
======================================================================
ERROR: prody.tests.proteins.test_pdbfile (unittest.loader._FailedTest.prody.tests.proteins.test_pdbfile)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_pdbfile
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_pdbfile.py", line 8, in <module>
import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_pdbfile.py", line 10, in <module>
from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
======================================================================
ERROR: prody.tests.proteins.test_wwpdb (unittest.loader._FailedTest.prody.tests.proteins.test_wwpdb)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_wwpdb
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_wwpdb.py", line 7, in <module>
import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_wwpdb.py", line 9, in <module>
from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
======================================================================
ERROR: prody.tests.sequence.test_msafile (unittest.loader._FailedTest.prody.tests.sequence.test_msafile)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.sequence.test_msafile
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence/test_msafile.py", line 8, in <module>
from numpy.testing import assert_array_equal, dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py)
----------------------------------------------------------------------
Ran 279 tests in 8.664s
FAILED (errors=15)
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build; python3.11 -m unittest discover -v
dh_auto_test: error: pybuild --test -i python{version} -p "3.12 3.11" returned exit code 13
make: *** [debian/rules:6: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202405/
About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large from AWS, using sbuild and a
reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
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