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.
