ctest failed

[Rumeza]

95% tests passed, 10 tests failed out of 212

Total Test time (real) = 8449.33 sec

The following tests FAILED: 52 - pyDepictor (Failed) 80 - pyChemReactions (Failed) 116 - pyTestGenerator (Failed) 117 - pyTestMHFP (Failed) 129 - pyDistGeomHelpers (Failed) 148 - pyMolHash (Failed) 168 - pyMolInterchange (Failed) 171 - pyGraphMolWrap (Timeout) 206 - pythonTestDirML (Failed) 212 - pythonTestDirChem (Timeout) Can you help me in resolving these failures.

[Rumeza]

Start 52: pyDepictor

52: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/Depictor/Wrap/testDepictor.py" 52: Test timeout computed to be: 1500 52: Traceback (most recent call last): 52: File "/home/farah/rdkit/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 113, in 52: class TestCase(unittest.TestCase): 52: File "/home/farah/rdkit/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 536, in TestCase 52: @unittest.skipIf(not rdDepictor.IsCoordGenSupportAvailable(), "CoordGen not available, skipping") 52: AttributeError: module 'rdkit.Chem.rdDepictor' has no attribute 'IsCoordGenSupportAvailable' 1/1 Test #52: pyDepictor .......................***Failed 3.57 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 3.76 sec

The following tests FAILED: 52 - pyDepictor (Failed)

[Rumeza]

Start 80: pyChemReactions

80: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" 80: Test timeout computed to be: 1500 80: [19:17:03] 80: 80: 80: Pre-condition Violation 80: getNumImplicitHs() called without preceding call to calcImplicitValence() 80: Violation occurred on line 297 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.cpp 80: Failed Expression: d_implicitValence > -1 80: 80: 80: [19:17:03] 80: 80: 80: Pre-condition Violation 80: getNumImplicitHs() called without preceding call to calcImplicitValence() 80: Violation occurred on line 297 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.cpp 80: Failed Expression: d_implicitValence > -1 80: 80: 80: ...[19:17:03] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 80: [19:17:03] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 80: [19:17:03] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 80: [19:17:03] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 80: .[19:17:03] product atom-mapping number 1 found multiple times. 80: FFF.F...F.......[19:17:03] mapped atoms in the reactants were not mapped in the products. 80: unmapped numbers are: 3 80: [19:17:03] mapped atoms in the reactants were not mapped in the products. 80: unmapped numbers are: 3 80: .[19:17:03] mapped atoms in the reactants were not mapped in the products. 80: unmapped numbers are: 3 80: ../home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:515: DeprecationWarning: Please use assertTrue instead. 80: self.failUnless(rxn) 80: [19:17:03] reactant 2 has no mapped atoms. 80: [19:17:03] reactant 2 has no mapped atoms. 80: [19:17:03] product 1 has no mapped atoms. 80: ../home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:558: DeprecationWarning: Please use assertEqual instead. 80: self.assertEquals(res, res2) 80: ......[19:17:03] SMARTS Parse Error: syntax error while parsing: C:1Q 80: [19:17:03] SMARTS Parse Error: Failed parsing SMARTS 'C:1Q' for input: 'C:1Q' 80: [19:17:03] SMARTS Parse Error: syntax error while parsing: C:1[N:3]Q 80: [19:17:03] SMARTS Parse Error: Failed parsing SMARTS 'C:1[N:3]Q' for input: 'C:1[N:3]Q' 80: .[19:17:03] reactant atom-mapping number 1 found multiple times. 80: [19:17:03] product atom-mapping number 2 not found in reactants. 80: [19:17:03] mapped atoms in the reactants were not mapped in the products. 80: unmapped numbers are: 4 80: [19:17:03] product atom-mapping number 5 not found in reactants. 80: ........./home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:739: DeprecationWarning: Please use assertFalse instead. 80: self.failIf(rxn is None) 80: /home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/home/farah/rdkit/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> 80: png = open(fname, 'rb').read() 80: ResourceWarning: Enable tracemalloc to get the object allocation traceback 80: ..[19:17:04] SMARTS Parse Error: syntax error while parsing: boromicacid 80: [19:17:04] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 80: [19:17:04] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 80: [19:17:04] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 80: [19:17:04] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 80: [19:17:04] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 80: [19:17:04] reaction has no reactants 80: [19:17:04] reaction has no products 80: [19:17:04] initialization failed 80: [19:17:04] reaction has no reactants 80: [19:17:04] reaction has no products 80: .[19:17:04] SMARTS Parse Error: syntax error while parsing: boromicacid 80: [19:17:05] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 80: [19:17:05] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 80: [19:17:05] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 80: [19:17:05] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 80: [19:17:05] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 80: [19:17:05] reaction has no reactants 80: [19:17:05] reaction has no products 80: [19:17:05] initialization failed 80: [19:17:05] reaction has no reactants 80: [19:17:05] reaction has no products 80: . 80: ====================================================================== 80: FAIL: test_reaction_copies_stereogroup (main.StereoGroupTests) 80: If multiple copies of an atom in StereoGroup show up in the product, they 80: ---------------------------------------------------------------------- 80: Traceback (most recent call last): 80: File "/home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 938, in test_reaction_copies_stereogroup 80: self.assertEqual( 80: AssertionError: 'CC(C)(OCCC@@HCC@@HBr)OCCC@@HCC@@HBr |&1:6,9,15,18|' != 'CC(C)(OCCC@HCC@HBr)OCCC@HCC@HBr |&1:6,9,15,18|' 80: - CC(C)(OCCC@@HCC@@HBr)OCCC@@HCC@@HBr |&1:6,9,15,18| 80: ? - - - - 80: + CC(C)(OCCC@HCC@HBr)OCCC@HCC@HBr |&1:6,9,15,18| 80: 80: 80: ====================================================================== 80: FAIL: test_reaction_defines_stereo (main.StereoGroupTests) 80: StereoGroup atoms are in the reaction, and the reaction creates the specified 80: ---------------------------------------------------------------------- 80: Traceback (most recent call last): 80: File "/home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 892, in test_reaction_defines_stereo 80: self.assertEqual(products, 'FC@@HC@HBr |&1:3|') 80: AssertionError: 'FC@@HC@@HBr |&1:3|' != 'FC@@HC@HBr |&1:3|' 80: - FC@@HC@@HBr |&1:3| 80: ? - 80: + FC@@HC@HBr |&1:3| 80: 80: 80: ====================================================================== 80: FAIL: test_reaction_destroys_stereo (main.StereoGroupTests) 80: StereoGroup atoms are in the reaction, and the reaction destroys the specified 80: ---------------------------------------------------------------------- 80: Traceback (most recent call last): 80: File "/home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 871, in test_reaction_destroys_stereo 80: self.assertEqual(products, 'FC(Cl)C@HBr |&1:3|') 80: AssertionError: 'FC(Cl)C@@HBr |&1:3|' != 'FC(Cl)C@HBr |&1:3|' 80: - FC(Cl)C@@HBr |&1:3| 80: ? - 80: + FC(Cl)C@HBr |&1:3| 80: 80: 80: ====================================================================== 80: FAIL: test_reaction_inverts_stereo (main.StereoGroupTests) 80: StereoGroup atoms are in the reaction, and the reaction inverts the specified 80: ---------------------------------------------------------------------- 80: Traceback (most recent call last): 80: File "/home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 848, in test_reaction_inverts_stereo 80: self.assertEqual(products, 'FC@HBr |o1:1|') 80: AssertionError: 'FC@@HBr |o1:1|' != 'FC@HBr |o1:1|' 80: - FC@@HBr |o1:1| 80: ? - 80: + FC@HBr |o1:1| 80: 80: 80: ====================================================================== 80: FAIL: test_stereogroup_is_spectator_to_reaction (main.StereoGroupTests) 80: StereoGroup atoms are not in the reaction 80: ---------------------------------------------------------------------- 80: Traceback (most recent call last): 80: File "/home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 905, in test_stereogroup_is_spectator_to_reaction 80: self.assertEqual(products, 'FC@HC@HBr |o1:3|') 80: AssertionError: 'FC@HC@@HBr |o1:3|' != 'FC@HC@HBr |o1:3|' 80: - FC@HC@@HBr |o1:3| 80: ? - 80: + FC@HC@HBr |o1:3|

Start 116: pyTestGenerator

116: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 116: Test timeout computed to be: 1500 116: F...E.E....E 116: ====================================================================== 116: ERROR: testFingerprintOptions (main.TestCase) 116: ---------------------------------------------------------------------- 116: Traceback (most recent call last): 116: File "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testGenerators.py", line 304, in testFingerprintOptions 116: g.GetOptions().numBitsPerFeature = 2 116: AttributeError: 'FingerprintGenerator64' object has no attribute 'GetOptions' 116: 116: ====================================================================== 116: ERROR: testMorganRedundantEnvironments (main.TestCase) 116: ---------------------------------------------------------------------- 116: Traceback (most recent call last): 116: File "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testGenerators.py", line 293, in testMorganRedundantEnvironments 116: g = rdFingerprintGenerator.GetMorganGenerator(2, includeRedundantEnvironments=True) 116: Boost.Python.ArgumentError: Python argument types in 116: rdkit.Chem.rdFingerprintGenerator.GetMorganGenerator(int) 116: did not match C++ signature: 116: GetMorganGenerator(unsigned int radius=3, bool countSimulation=False, bool includeChirality=False, bool useBondTypes=True, bool onlyNonzeroInvariants=False, bool includeRingMembership=True, boost::python::api::object {lvalue} countBounds=None, unsigned int fpSize=2048, boost::python::api::object {lvalue} atomInvariantsGenerator=None, boost::python::api::object {lvalue} bondInvariantsGenerator=None) 116: 116: ====================================================================== 116: ERROR: testTopologicalTorsionShortestPaths (main.TestCase) 116: ---------------------------------------------------------------------- 116: Traceback (most recent call last): 116: File "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testGenerators.py", line 338, in testTopologicalTorsionShortestPaths 116: g.GetOptions().onlyShortestPaths = True 116: AttributeError: 'FingerprintGenerator64' object has no attribute 'GetOptions' 116: 116: ====================================================================== 116: FAIL: testAdditionalOutput (main.TestCase) 116: ---------------------------------------------------------------------- 116: Traceback (most recent call last): 116: File "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testGenerators.py", line 231, in testAdditionalOutput 116: self.assertEqual(ao.GetAtomToBits(), ((1404, 1916), (1404, 1596), (1596, 1916))) 116: AssertionError: Tuples differ: ((351, 479), (351, 399), (479, 399)) != ((1404, 1916), (1404, 1596), (1596, 1916)) 116: 116: First differing element 0: 116: (351, 479) 116: (1404, 1916) 116: 116: - ((351, 479), (351, 399), (479, 399)) 116: + ((1404, 1916), (1404, 1596), (1596, 1916)) 116: 116: ---------------------------------------------------------------------- 116: Ran 12 tests in 0.637s 116: 116: FAILED (failures=1, errors=3) 1/1 Test #116: pyTestGenerator ..................***Failed 4.16 sec

Start 117: pyTestMHFP

117: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 117: Test timeout computed to be: 1500 117: FF 117: ====================================================================== 117: FAIL: testMHFPDistance (main.TestCase) 117: ---------------------------------------------------------------------- 117: Traceback (most recent call last): 117: File "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testMHFP.py", line 25, in testMHFPDistance 117: self.assertEqual(dist, 0.0) 117: AssertionError: 1.0 != 0.0 117: 117: ====================================================================== 117: FAIL: testMHFPFingerprint (main.TestCase) 117: ---------------------------------------------------------------------- 117: Traceback (most recent call last): 117: File "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testMHFP.py", line 50, in testMHFPFingerprint 117: self.assertEqual(dist, 0.5390625) 117: AssertionError: 0.4609375 != 0.5390625 117: 117: ---------------------------------------------------------------------- 117: Ran 2 tests in 0.388s 117: 117: FAILED (failures=2) 1/1 Test #117: pyTestMHFP .......................***Failed 2.97 sec

Start 129: pyDistGeomHelpers

129: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 129: Test timeout computed to be: 1500 129: .[19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: ..[19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: ..[19:36:52] Molecule does not have explicit Hs. Consider calling AddHs() 129: .[19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:56] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:56] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:56] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:56] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:56] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:56] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:57] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:57] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:57] Molecule does not have explicit Hs. Consider calling AddHs() 129: .[19:36:57] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:36:58] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:37:00] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:37:01] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:37:03] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:37:05] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:37:12] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:37:13] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:37:15] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:37:16] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:37:20] Molecule does not have explicit Hs. Consider calling AddHs() 129: [19:37:22] Molecule does not have explicit Hs. Consider calling AddHs() 129: .[19:37:31] Molecule does not have explicit Hs. Consider calling AddHs()

Start 148: pyMolHash

148: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/MolHash/Wrap/testMolHash.py" 148: Test timeout computed to be: 1500 148: .F 148: ====================================================================== 148: FAIL: testCxSmiles (main.TestCase) 148: ---------------------------------------------------------------------- 148: Traceback (most recent call last): 148: File "/home/farah/rdkit/Code/GraphMol/MolHash/Wrap/testMolHash.py", line 42, in testCxSmiles 148: self.assertEqual(rdMolHash.MolHash(m, rdMolHash.HashFunction.HetAtomTautomer), 148: AssertionError: 'CC@HC@@HCC([C]1[CH][N][CH][N]1)[C]1[CH][N][CH][N]1_3_0' != 'CC@HC@@HC@H[O]_3_0' 148: - CC@HC@@HCC([C]1[CH][N][CH][N]1)[C]1[CH][N][CH][N]1_3_0 148: + CC@HC@@HC@H[O]_3_0 148: 148: 148: ---------------------------------------------------------------------- 148: Ran 2 tests in 0.183s 148: 148: FAILED (failures=1) 1/1 Test #148: pyMolHash ........................***Failed 2.65 sec

Start 168: pyMolInterchange

168: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 168: Test timeout computed to be: 1500 168: .F 168: ====================================================================== 168: FAIL: test2 (main.TestCase) 168: ---------------------------------------------------------------------- 168: Traceback (most recent call last): 168: File "/home/farah/rdkit/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py", line 33, in test2 168: self.assertIn('stereoGroups',json) 168: AssertionError: 'stereoGroups' not found in '{"commonchem":{"version":10},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":1,"stereo":"ccw"},{"z":8,"impHs":1},{"impHs":2},{"impHs":1,"stereo":"cw"},{"impHs":3},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,6]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2022.09.4","cipRanks":[0,3,5,2,4,1,6],"cipCodes":[[1,"S"],[4,"R"]]}]}]}' 168: 168: ---------------------------------------------------------------------- 168: Ran 2 tests in 0.263s 168: 168: FAILED (failures=1) 1/1 Test #168: pyMolInterchange .................***Failed 3.70 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 3.90 sec

The following tests FAILED: 168 - pyMolInterchange (Failed)

Start 171: pyGraphMolWrap

171: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/Wrap/rough_test.py" 171: Test timeout computed to be: 1500 171: ..............[19:50:54] SMARTS Parse Error: syntax error while parsing: fiib 171: [19:50:54] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' 171: ....[19:50:54] ERROR: Problems encountered parsing data fields 171: [19:50:54] ERROR: moving to the beginning of the next molecule 171: [19:50:54] ERROR: Problems encountered parsing data fields 171: [19:50:54] ERROR: moving to the beginning of the next molecule 171: [19:50:54] Spurious data before the first property will be ignored 171: [19:50:54] Property will be truncated after the first blank line 171: [19:50:54] Property will be truncated after the first blank line 171: [19:50:54] Property will be truncated after the first blank line 171: [19:50:54] ERROR: Problems encountered parsing data fields 171: [19:50:54] ERROR: moving to the beginning of the next molecule 171: [19:50:54] ERROR: Problems encountered parsing data fields 171: [19:50:54] ERROR: moving to the beginning of the next molecule 171: [19:50:54] Spurious data before the first property will be ignored 171: [19:50:54] Property will be truncated after the first blank line 171: [19:50:54] Property will be truncated after the first blank line 171: [19:50:54] Property will be truncated after the first blank line 171: [19:50:54] ERROR: Problems encountered parsing data fields 171: [19:50:54] ERROR: moving to the beginning of the next molecule 171: [19:50:54] Property will be truncated after the first blank line 171: [19:50:54] ERROR: Problems encountered parsing data fields 171: [19:50:54] ERROR: moving to the beginning of the next molecule 171: [19:50:54] Property will be truncated after the first blank line 171: .[19:50:54] SMILES Parse Error: syntax error while parsing: fail 171: [19:50:54] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' 171: [19:50:54] ERROR: Smiles parse error on line 2 171: [19:50:54] ERROR: Cannot create molecule from : 'fail' 171: >>> This may result in an infinite loop. It should finish almost instantly 171: <<< OK, it finished. 171: ............[19:50:55] Explicit valence for atom # 1 C, 5, is greater than permitted 171: ........../home/farah/rdkit/Code/GraphMol/Wrap/rough_test.py:2155: DeprecationWarning: Please use assertEqual instead. 171: self.assertEquals(ri.AtomRingFamilies(), ()) 171: ..[19:50:55] non-ring atom 0 marked aromatic 171: [19:50:55] non-ring atom 0 marked aromatic 171: [19:50:55] 171: 171: 171: Range Error 171: idx 171: Violation occurred on line 213 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/ROMol.cpp 171: Failed Expression: 12 < 6 171: 171: 171: [19:50:55] non-ring atom 0 marked aromatic 171: [19:50:55] non-ring atom 0 marked aromatic 171: [19:50:55] 171: 171: 171: Range Error 171: idx 171: Violation occurred on line 213 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/ROMol.cpp 171: Failed Expression: 12 < 6 171: 171: 171: ...............[19:50:56] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. 171: [19:50:56] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. 171: ..............[19:50:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 171: [19:50:56] Explicit valence for atom # 1 C, 5, is greater than permitted 171: ...........................[19:51:44] unable to set wavy bonds for double bonds: 3 171: .........[19:51:44] 171: 171: 171: Range Error 171: idx 171: Violation occurred on line 213 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/ROMol.cpp 171: Failed Expression: 6 < 5 171: 171: 171: ...................[19:52:02] Explicit valence for atom # 1 F, 2, is greater than permitted 171: [19:52:02] Explicit valence for atom # 6 F, 2, is greater than permitted 171: [19:52:02] Can't kekulize mol. Unkekulized atoms: 3 4 5 171: .[19:52:02] Warning: molecule is tagged as 3D, but all Z coords are zero 171: [19:52:02] Warning: molecule is tagged as 3D, but all Z coords are zero 171: [19:52:02] Warning: molecule is tagged as 3D, but all Z coords are zero 171: [19:52:03] Warning: molecule is tagged as 3D, but all Z coords are zero 171: [19:52:03] Warning: molecule is tagged as 3D, but all Z coords are zero 171: [19:52:03] Warning: molecule is tagged as 3D, but all Z coords are zero 171: ...............[19:52:35] 171: 171: 171: Pre-condition Violation 171: no owner 171: Violation occurred on line 138 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.h 171: Failed Expression: dp_mol 171: 171: 171: [19:52:35] 171: 171: 171: Pre-condition Violation 171: no owner 171: Violation occurred on line 138 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.h 171: Failed Expression: dp_mol 171: 171: 171: [19:52:35] 171: 171: 171: Pre-condition Violation 171: no owner 171: Violation occurred on line 138 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.h 171: Failed Expression: dp_mol 171: 171: 171: [19:52:35] 171: 171: 171: Pre-condition Violation 171: no owner 171: Violation occurred on line 138 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.h 171: Failed Expression: dp_mol 171: 171: 171: [19:52:35] 171: 171: 171: Pre-condition Violation 171: no owner 171: Violation occurred on line 138 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.h 171: Failed Expression: dp_mol 171: 171: 171: .....[19:52:35] 171: 171: 171: Range Error 171: atomIdx1 171: Violation occurred on line 331 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/RWMol.cpp 171: Failed Expression: 0 < 0 171: 171: 171: ......[19:52:35] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 171: [19:52:35] ERROR: Smiles parse error on line 0 171: [19:52:35] ERROR: Cannot create molecule from : 'c1ccccc' 171: [19:52:35] SMILES Parse Error: extra open parentheses for input: 'C(C' 171: [19:52:35] ERROR: Smiles parse error on line 3 171: [19:52:35] ERROR: Cannot create molecule from : 'C(C' 171: [19:52:35] Explicit valence for atom # 1 C, 5, is greater than permitted 171: [19:52:35] ERROR: Could not sanitize molecule on line 6 171: [19:52:35] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted 171: [19:52:35] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 171: [19:52:35] ERROR: Smiles parse error on line 0 171: [19:52:35] ERROR: Cannot create molecule from : 'c1ccccc' 171: [19:52:35] SMILES Parse Error: extra open parentheses for input: 'C(C' 171: [19:52:35] ERROR: Smiles parse error on line 3 171: [19:52:35] ERROR: Cannot create molecule from : 'C(C' 171: [19:52:35] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' 171: [19:52:35] ERROR: Smiles parse error on line 6 171: [19:52:35] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' 171: [19:52:35] Explicit valence for atom # 1 F, 2, is greater than permitted 171: [19:52:35] ERROR: Could not sanitize molecule ending on line 21 171: [19:52:35] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 171: [19:52:35] ERROR: EOF hit while reading atoms 171: [19:52:35] ERROR: moving to the beginning of the next molecule 171: [19:52:35] Explicit valence for atom # 1 F, 2, is greater than permitted 171: [19:52:35] ERROR: Could not sanitize molecule ending on line 21 171: [19:52:35] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 171: [19:52:35] ERROR: EOF hit while reading atoms 171: [19:52:35] ERROR: moving to the beginning of the next molecule 171: ....[19:52:36] 171: 171: 171: Pre-condition Violation 171: RingInfo not initialized 171: Violation occurred on line 169 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/RingInfo.cpp 171: Failed Expression: df_init 171: 1/1 Test #171: pyGraphMolWrap ...................***Timeout 1500.18 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 1500.39 sec

Start 206: pythonTestDirML

206: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/rdkit/ML/test_list.py" "--testDir" "/home/farah/rdkit/rdkit/ML" 206: Test timeout computed to be: 1500 206: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/Data/SplitData.py:124: DeprecationWarning: The random parameter to shuffle() has been deprecated 206: since Python 3.9 and will be removed in a subsequent version. 206: random.shuffle(perm, random=random.random) 206: ....... 206: ---------------------------------------------------------------------- 206: Ran 7 tests in 6.200s 206: 206: OK 206: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/ScreenComposite.py:429: DeprecationWarning: [np.int](http://np.int/) is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing [np.int](http://np.int/), you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information. 206: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 206: voteTab = numpy.zeros((nResultCodes, nResultCodes), numpy.int) 206: ./home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/Data/SplitData.py:124: DeprecationWarning: The random parameter to shuffle() has been deprecated 206: since Python 3.9 and will be removed in a subsequent version. 206: random.shuffle(perm, random=random.random) 206: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/Data/DataUtils.py:68: DeprecationWarning: The random parameter to shuffle() has been deprecated 206: since Python 3.9 and will be removed in a subsequent version. 206: random.shuffle(res, random=random.random) 206: ......../home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/Data/DataUtils.py:655: DeprecationWarning: The random parameter to shuffle() has been deprecated 206: since Python 3.9 and will be removed in a subsequent version. 206: random.shuffle(acts, random=random.random) 206: ... 206: ---------------------------------------------------------------------- 206: Ran 12 tests in 1.039s 206: 206: OK 206: . 206: ---------------------------------------------------------------------- 206: Ran 1 test in 0.385s 206: 206: OK 206: ... 206: ---------------------------------------------------------------------- 206: Ran 3 tests in 0.018s 206: 206: OK 206: ........ 206: ---------------------------------------------------------------------- 206: Ran 8 tests in 0.015s 206: 206: OK 206: .... 206: ---------------------------------------------------------------------- 206: Ran 4 tests in 4.527s 206: 206: OK 206: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/Data/DataUtils.py:68: DeprecationWarning: The random parameter to shuffle() has been deprecated 206: since Python 3.9 and will be removed in a subsequent version. 206: random.shuffle(res, random=random.random) 206: ..... 206: ---------------------------------------------------------------------- 206: Ran 5 tests in 0.022s 206: 206: OK 206: ......./home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/Data/DataUtils.py:655: DeprecationWarning: The random parameter to shuffle() has been deprecated 206: since Python 3.9 and will be removed in a subsequent version. 206: random.shuffle(acts, random=random.random) 206: .. 206: ---------------------------------------------------------------------- 206: Ran 9 tests in 0.033s 206: 206: OK 206: ............ 206: ---------------------------------------------------------------------- 206: Ran 12 tests in 0.028s 206: 206: OK 206: ..... 206: ---------------------------------------------------------------------- 206: Ran 5 tests in 0.467s 206: 206: OK 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 208, in main.SplitDbData 206: Failed example: 206: train,test = SplitDbData(conn,1./3.,'basic_2class') 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main.SplitDbData[5]>", line 1, in 206: train,test = SplitDbData(conn,1./3.,'basic_2class') 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 261, in SplitDbData 206: train, test = SplitIndices(nRes, frac, silent=1) 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 206: RDRandom.shuffle(perm, random=random.random) 206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle' 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 209, in main.SplitDbData 206: Failed example: 206: [str(x) for x in train] 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main.SplitDbData[6]>", line 1, in 206: [str(x) for x in train] 206: NameError: name 'train' is not defined 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 214, in main__.SplitDbData 206: Failed example: 206: train,test = SplitDbData(conn,.5,'basic_2class',useActs=1) 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main.SplitDbData[8]>", line 1, in 206: train,test = SplitDbData(conn,.5,'basic_2class',useActs=1) 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 289, in SplitDbData 206: train, test = SplitIndices(nRes, frac, silent=1) 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 206: RDRandom.shuffle(perm, random=random.random) 206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle' 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 215, in main.SplitDbData 206: Failed example: 206: [str(x) for x in train] 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main.SplitDbData[9]>", line 1, in 206: [str(x) for x in train] 206: NameError: name 'train' is not defined 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 223, in main.SplitDbData 206: Failed example: 206: train,test = SplitDbData(conn,[.5,1./3.],'basic_2class',useActs=1) 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main__.SplitDbData[11]>", line 1, in 206: train,test = SplitDbData(conn,[.5,1./3.],'basic_2class',useActs=1) 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 289, in SplitDbData 206: train, test = SplitIndices(nRes, frac, silent=1) 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 206: RDRandom.shuffle(perm, random=random.random) 206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle' 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 224, in main.SplitDbData 206: Failed example: 206: [str(x) for x in train] 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main.SplitDbData[12]>", line 1, in 206: [str(x) for x in train] 206: NameError: name 'train' is not defined 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 230, in main.SplitDbData 206: Failed example: 206: train,test = SplitDbData(conn,.5,'float_2class',useActs=1,actBounds=[1.0]) 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main.SplitDbData[14]>", line 1, in 206: train,test = SplitDbData(conn,.5,'float_2class',useActs=1,actBounds=[1.0]) 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 289, in SplitDbData 206: train, test = SplitIndices(nRes, frac, silent=1) 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 206: RDRandom.shuffle(perm, random=random.random) 206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle' 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 231, in main.SplitDbData 206: Failed example: 206: [str(x) for x in train] 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main.SplitDbData[15]>", line 1, in 206: [str(x) for x in train] 206: NameError: name 'train' is not defined 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 54, in main.SplitIndices 206: Failed example: 206: test,train = SplitIndices(10,.5) 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main.SplitIndices[2]>", line 1, in 206: test,train = SplitIndices(10,.5) 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 206: RDRandom.shuffle(perm, random=random.random) 206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle' 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 55, in main.SplitIndices 206: Failed example: 206: test 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main.SplitIndices[3]>", line 1, in 206: test 206: NameError: name 'test' is not defined 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 57, in main.SplitIndices 206: Failed example: 206: train 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main.SplitIndices[4]>", line 1, in 206: train 206: NameError: name 'train' is not defined 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 60, in main.SplitIndices 206: Failed example: 206: test,train = SplitIndices(10,.5) 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main.SplitIndices[5]>", line 1, in 206: test,train = SplitIndices(10,.5) 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 206: RDRandom.shuffle(perm, random=random.random) 206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle' 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 61, in main.SplitIndices 206: Failed example: 206: test 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main.SplitIndices[6]>", line 1, in 206: test 206: NameError: name 'test' is not defined 206: ** 206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 63, in main.SplitIndices 206: Failed example: 206: train 206: Exception raised: 206: Traceback (most recent call last): 206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 206: exec(compile(example.source, filename, "single", 206: File "<doctest main.SplitIndices[7]>", line 1, in 206: train 206: NameError: name 'train' is not defined 206: ** 206: 2 items had failures: 206: 8 of 16 in main.SplitDbData 206: 6 of 22 in main.SplitIndices 206: Test Failed 14 failures. 206: !!! TEST FAILURE: python SplitData.py {} 206: . 206: ---------------------------------------------------------------------- 206: Ran 1 test in 0.025s 206: 206: OK 206: ...... 206: ---------------------------------------------------------------------- 206: Ran 6 tests in 0.023s 206: 206: OK 206: .... 206: ---------------------------------------------------------------------- 206: Ran 4 tests in 10.162s 206: 206: OK 206: ...... 206: ---------------------------------------------------------------------- 206: Ran 6 tests in 0.180s 206: 206: OK 206: .. 206: ---------------------------------------------------------------------- 206: Ran 2 tests in 1.432s 206: 206: OK 206: ......../home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/DecTree/BuildQuantTree.py:34: DeprecationWarning: The random parameter to shuffle() has been deprecated 206: since Python 3.9 and will be removed in a subsequent version. 206: random.shuffle(ids, random=random.random) 206: .. 206: ---------------------------------------------------------------------- 206: Ran 10 tests in 0.133s 206: 206: OK 206: ..... 206: ---------------------------------------------------------------------- 206: Ran 5 tests in 0.913s 206: 206: OK 206: .. 206: ---------------------------------------------------------------------- 206: Ran 2 tests in 0.035s 206: 206: OK 206: ..... 206: ---------------------------------------------------------------------- 206: Ran 5 tests in 0.096s 206: 206: OK 206: ... 206: ---------------------------------------------------------------------- 206: Ran 3 tests in 0.089s 206: 206: OK 206: EEE 206: ====================================================================== 206: ERROR: test0CorrMat (main.TestCase) 206: ---------------------------------------------------------------------- 206: Traceback (most recent call last): 206: File "/home/farah/rdkit/rdkit/ML/InfoTheory/UnitTestCorrMatGen.py", line 48, in setUp 206: random.shuffle(obits, random=random.random) 206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle' 206: 206: ====================================================================== 206: ERROR: test1Cluster (main__.TestCase) 206: ---------------------------------------------------------------------- 206: Traceback (most recent call last): 206: File "/home/farah/rdkit/rdkit/ML/InfoTheory/UnitTestCorrMatGen.py", line 48, in setUp 206: random.shuffle(obits, random=random.random) 206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle' 206: 206: ====================================================================== 206: ERROR: test_getValLTM (main.TestCase) 206: ---------------------------------------------------------------------- 206: Traceback (most recent call last): 206: File "/home/farah/rdkit/rdkit/ML/InfoTheory/UnitTestCorrMatGen.py", line 48, in setUp 206: random.shuffle(obits, random=random.random) 206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle' 206: 206: ---------------------------------------------------------------------- 206: Ran 3 tests in 0.007s 206: 206: FAILED (errors=3) 206: !!! TEST FAILURE: python UnitTestCorrMatGen.py {} 206: ...... 206: ---------------------------------------------------------------------- 206: Ran 6 tests in 4.945s 206: 206: OK 206: ...EE.. 206: ====================================================================== 206: ERROR: testPerm1 (main.TestCase) 206: ---------------------------------------------------------------------- 206: Traceback (most recent call last): 206: File "/home/farah/rdkit/rdkit/ML/ModelPackage/UnitTestPackage.py", line 101, in testPerm1 206: random.shuffle(perm, random=random.random) 206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle' 206: 206: ====================================================================== 206: ERROR: testPerm2 (main__.TestCase) 206: ---------------------------------------------------------------------- 206: Traceback (most recent call last): 206: File "/home/farah/rdkit/rdkit/ML/ModelPackage/UnitTestPackage.py", line 117, in testPerm2 206: random.shuffle(perm, random=random.random) 206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle' 206: 206: ---------------------------------------------------------------------- 206: Ran 7 tests in 0.847s 206: 206: FAILED (errors=2) 206: !!! TEST FAILURE: python UnitTestPackage.py {} 206: .... 206: ---------------------------------------------------------------------- 206: Ran 4 tests in 0.117s 206: 206: OK 206: ..... 206: ---------------------------------------------------------------------- 206: Ran 5 tests in 32.179s 206: 206: OK 206: .... 206: ---------------------------------------------------------------------- 206: Ran 4 tests in 0.013s 206: 206: OK 206: .... 206: ---------------------------------------------------------------------- 206: Ran 4 tests in 0.007s 206: 206: OK 206: .... 206: ---------------------------------------------------------------------- 206: Ran 4 tests in 0.049s 206: 206: OK 206: !!! TEST FAILURE: python test_list.py {'dir': 'Data'} 206: !!! TEST FAILURE: python test_list.py {'dir': 'InfoTheory'} 206: !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} 1/1 Test #206: pythonTestDirML ..................***Failed 141.58 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 141.89 sec

The following tests FAILED: 206 - pythonTestDirML (Failed)

[Rumeza]

Start 212: pythonTestDirChem

212: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/rdkit/Chem/test_list.py" "--testDir" "/home/farah/rdkit/rdkit/Chem" "--buildType" "Release" 212: Test timeout computed to be: 1500 212: ....... 212: ---------------------------------------------------------------------- 212: Ran 7 tests in 1.748s 212: 212: OK 212: ...... 212: ---------------------------------------------------------------------- 212: Ran 6 tests in 0.770s 212: 212: OK 212: ....[20:26:27] 212: 212: 212: Pre-condition Violation 212: valence not defined for atoms not associated with molecules 212: Violation occurred on line 423 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.cpp 212: Failed Expression: dp_mol 212: 212: 212: . 212: ---------------------------------------------------------------------- 212: Ran 5 tests in 0.227s 212: 212: OK 212: .... 212: ---------------------------------------------------------------------- 212: Ran 4 tests in 0.230s 212: 212: OK 212: .. 212: ---------------------------------------------------------------------- 212: Ran 2 tests in 0.166s 212: 212: OK 212: ...................... 212: ---------------------------------------------------------------------- 212: Ran 22 tests in 0.422s 212: 212: OK 212: .....s..........E......ss 212: ====================================================================== 212: ERROR: testIpc (main.TestCase) 212: ---------------------------------------------------------------------- 212: Traceback (most recent call last): 212: File "/home/farah/rdkit/rdkit/Chem/UnitTestGraphDescriptors_2.py", line 117, in testIpc 212: avgIpc = GraphDescriptors.AvgIpc(m, forceDMat=1) 212: AttributeError: module 'rdkit.Chem.GraphDescriptors' has no attribute 'AvgIpc' 212: 212: ---------------------------------------------------------------------- 212: Ran 25 tests in 1.884s 212: 212: FAILED (errors=1, skipped=3) 212: ..s 212: ---------------------------------------------------------------------- 212: Ran 3 tests in 2.072s 212: 212: OK (skipped=1) 212: ................................... 212: ---------------------------------------------------------------------- 212: Ran 35 tests in 1.462s 212: 212: OK 212: .... 212: ---------------------------------------------------------------------- 212: Ran 4 tests in 0.543s 212: 212: OK 212: . 212: ---------------------------------------------------------------------- 212: Ran 1 test in 0.401s 212: 212: OK 212: ....... 212: ---------------------------------------------------------------------- 212: Ran 7 tests in 1.113s 212: 212: OK 212: ... 212: ---------------------------------------------------------------------- 212: Ran 3 tests in 1.323s 212: 212: OK 212: .ss.ss....... 212: ---------------------------------------------------------------------- 212: Ran 13 tests in 24.496s 212: 212: OK (skipped=4) 212: [20:27:51] Molecule does not have explicit Hs. Consider calling AddHs() 212: .[20:27:52] Molecule does not have explicit Hs. Consider calling AddHs() 212: ..............F....[20:37:28] WARNING: More than one matching pattern found - picking one 212: 212: [20:37:29] WARNING: More than one matching pattern found - picking one 212: 212: .[20:37:29] WARNING: More than one matching pattern found - picking one 212: 212: ... 212: ====================================================================== 212: FAIL: testGithub6045 (main.TestCase) 212: ---------------------------------------------------------------------- 212: Traceback (most recent call last): 212: File "/home/farah/rdkit/rdkit/Chem/UnitTestMol3D.py", line 471, in testGithub6045 212: self.assertEqual(len(prod.GetStereoGroups()), 0) 212: AssertionError: 1 != 0 212: 212: ---------------------------------------------------------------------- 212: Ran 24 tests in 617.382s 212: 212: FAILED (failures=1) 212: {'C/C(F)=C/C@@HCl', 'C/C(F)=C/C@HCl', 'C/C(F)=C\C@@HCl', 'C/C(F)=C\C@HCl'} 212: {'C/C(F)=C/C@@HCl', 'C/C(F)=C/C@HCl', 'C/C(F)=C\C@@HCl', 'C/C(F)=C\C@HCl'} 212: {'FC@HC@@HCl', 'FC@@HC@@HCl', 'FC@HC@HCl'} 212: !!!! ['CC@HC@@HF', 'CC@@HC@@HBr', 'CC@@HC@@HF', 'CC@HC@@HBr', 'CC@@HC@HBr', 'CC@@HC@@HBr', 'CC@HC@HBr', 'CC@HC@@HBr'] 212: ...../home/farah/anaconda3/lib/python3.9/site-packages/rdkit/Chem/BuildFragmentCatalog.py:164: DeprecationWarning: [np.int](http://np.int/) is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing [np.int](http://np.int/), you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information. 212: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 212: resTbl = numpy.zeros((nBits, 2, nActs), numpy.int) 212: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/Chem/BuildFragmentCatalog.py:228: DeprecationWarning: [np.int](http://np.int/) is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing [np.int](http://np.int/), you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information. 212: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 212: resTbl = numpy.zeros((nBits, 2, nActs), numpy.int) 212: ... 212: ---------------------------------------------------------------------- 212: Ran 8 tests in 1.551s 212: 212: OK 212: .E...[20:38:49] WARNING: not removing hydrogen atom without neighbors 212: [20:38:50] WARNING: not removing hydrogen atom without neighbors 212: [20:38:50] WARNING: not removing hydrogen atom without neighbors 212: ....[20:38:50] WARNING: not removing hydrogen atom without neighbors 212: ...... 212: ====================================================================== 212: ERROR: testGetMolDescriptors (main.TestCase) 212: ---------------------------------------------------------------------- 212: Traceback (most recent call last): 212: File "/home/farah/rdkit/rdkit/Chem/UnitTestDescriptors.py", line 204, in testGetMolDescriptors 212: descs = Descriptors.CalcMolDescriptors(mol) 212: AttributeError: module 'rdkit.Chem.Descriptors' has no attribute 'CalcMolDescriptors' 212: 212: ---------------------------------------------------------------------- 212: Ran 15 tests in 34.707s 212: 212: FAILED (errors=1) 212: [20:38:53] WARNING: Omitted undefined stereo 212: 212: [20:38:53] WARNING: Proton(s) added/removed 212: 212: ....... 212: ---------------------------------------------------------------------- 212: Ran 7 tests in 125.984s 212: 212: OK 212: 212: InChI write Summary: 1162 identical, 0 suffix variance, 19 reasonable 212: 212: InChI read Summary: 685 identical, 0 variance, 496 reasonable variance 212: .... 212: ---------------------------------------------------------------------- 212: Ran 4 tests in 22.631s 212: 212: OK 212: ...... 212: ---------------------------------------------------------------------- 212: Ran 6 tests in 6.663s 212: 212: OK 212: .......<doctest rdkit.Chem.PandasTools[5]>:1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. 212: antibiotics = antibiotics.append({'Smiles':'CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C', 212: <doctest rdkit.Chem.PandasTools[6]>:1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. 212: antibiotics = antibiotics.append({ 212: <doctest rdkit.Chem.PandasTools[7]>:1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. 212: antibiotics = antibiotics.append({ 212: .................E.. 212: ====================================================================== 212: ERROR: test_write_V3000_to_sdf (main.TestWriteSDF) 212: ---------------------------------------------------------------------- 212: Traceback (most recent call last): 212: File "/home/farah/rdkit/rdkit/Chem/UnitTestPandasTools.py", line 351, in test_write_V3000_to_sdf 212: PandasTools.WriteSDF(self.df, filename, forceV3000=True) 212: TypeError: WriteSDF() got an unexpected keyword argument 'forceV3000' 212: 212: ---------------------------------------------------------------------- 212: Ran 27 tests in 27.735s 212: 212: FAILED (errors=1) 212: ............./home/farah/anaconda3/lib/python3.9/site-packages/rdkit/Chem/BRICS.py:291: DeprecationWarning: The random parameter to shuffle() has been deprecated 212: since Python 3.9 and will be removed in a subsequent version. 212: random.shuffle(indices, random=random.random) 212: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/Chem/BRICS.py:299: DeprecationWarning: The random parameter to shuffle() has been deprecated 212: since Python 3.9 and will be removed in a subsequent version. 212: random.shuffle(compats, random=random.random) 212: .[20:44:08] WARNING: More than one matching pattern found - picking one 212: 212: [20:44:08] WARNING: More than one matching pattern found - picking one 212: 212: ..[20:44:10] Molecule does not have explicit Hs. Consider calling AddHs() 212: [20:44:10] Molecule does not have explicit Hs. Consider calling AddHs() 212: [20:44:10] Molecule does not have explicit Hs. Consider calling AddHs() 212: [20:44:10] Molecule does not have explicit Hs. Consider calling AddHs() 212: ......... 212: ---------------------------------------------------------------------- 212: Ran 25 tests in 111.015s 212: 212: OK 212: .. 212: ---------------------------------------------------------------------- 212: Ran 2 tests in 1.228s 212: 212: OK 212: ..s... 212: ---------------------------------------------------------------------- 212: Ran 6 tests in 9.538s 212: 212: OK (skipped=1) 212: ** 212: File "/home/farah/rdkit/rdkit/Chem/BRICS.py", line 255, in main.FindBRICSBonds 212: Failed example: 212: res = list(FindBRICSBonds(m,randomizeOrder=True)) 212: Exception raised: 212: Traceback (most recent call last): 212: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in run 212: exec(compile(example.source, filename, "single", 212: File "<doctest main.FindBRICSBonds[8]>", line 1, in 212: res = list(FindBRICSBonds(m,randomizeOrder=True)) 212: File "/home/farah/rdkit/rdkit/Chem/BRICS.py", line 290, in FindBRICSBonds 212: random.shuffle(indices, random=random.random) 212: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle' 212: ** 212: 1 items had failures: 212: 1 of 20 in main__.FindBRICSBonds 212: Test Failed 1 failures. 212: ..[20:46:37] WARNING: not removing hydrogen atom without neighbors 212: .[20:46:37] WARNING: not removing hydrogen atom without neighbors 212: .[20:46:38] WARNING: no name column found on line 1 212: [20:46:38] WARNING: no name column found on line 2 212: [20:46:38] WARNING: no name column found on line 3 212: [20:46:38] WARNING: no name column found on line 4 212: [20:46:38] WARNING: no name column found on line 5 212: [20:46:38] WARNING: no name column found on line 6 212: [20:46:38] WARNING: no name column found on line 7 212: [20:46:38] WARNING: no name column found on line 8 212: [20:46:38] WARNING: no name column found on line 9 212: [20:46:38] WARNING: no name column found on line 10 212: [20:46:38] WARNING: no name column found on line 11 212: [20:46:38] 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[20:46:38] WARNING: no name column found on line 134 212: [20:46:38] WARNING: no name column found on line 135 212: [20:46:38] WARNING: no name column found on line 136 212: [20:46:38] WARNING: no name column found on line 137 212: [20:46:38] WARNING: no name column found on line 138 212: [20:46:38] WARNING: no name column found on line 139 212: [20:46:38] WARNING: no name column found on line 140 212: [20:46:38] WARNING: no name column found on line 141 212: [20:46:38] WARNING: no name column found on line 142 212: [20:46:38] WARNING: no name column found on line 143 212: [20:46:38] WARNING: no name column found on line 144 212: [20:46:38] WARNING: no name column found on line 145 212: [20:46:38] WARNING: no name column found on line 146 212: [20:46:38] WARNING: no name column found on line 147 212: [20:46:38] WARNING: no name column found on line 148 212: [20:46:38] WARNING: no name column found on line 149 212: [20:46:38] WARNING: no name column found on line 150 212: [20:46:38] 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name column found on line 168 212: [20:46:38] WARNING: no name column found on line 169 212: [20:46:38] WARNING: no name column found on line 170 212: [20:46:38] WARNING: no name column found on line 171 212: [20:46:38] WARNING: no name column found on line 172 212: [20:46:38] WARNING: no name column found on line 173 212: [20:46:38] WARNING: no name column found on line 174 212: [20:46:38] WARNING: no name column found on line 175 212: [20:46:38] WARNING: no name column found on line 176 212: [20:46:38] WARNING: no name column found on line 177 212: [20:46:38] WARNING: no name column found on line 178 212: [20:46:38] WARNING: no name column found on line 179 212: [20:46:38] WARNING: no name column found on line 180 212: [20:46:38] WARNING: no name column found on line 181 212: [20:46:38] WARNING: no name column found on line 182 212: [20:46:38] WARNING: no name column found on line 183 212: [20:46:38] WARNING: no name column found on line 184 212: [20:46:38] WARNING: no name column found on line 185 212: [20:46:38] WARNING: no name column found on line 186 212: [20:46:38] WARNING: no name column found on line 187 212: [20:46:38] WARNING: no name column found on line 188 212: [20:46:38] WARNING: no name column found on line 189 212: [20:46:38] WARNING: no name column found on line 190 212: [20:46:38] WARNING: no name column found on line 191 212: [20:46:38] WARNING: no name column found on line 192 212: [20:46:38] WARNING: no name column found on line 193 212: [20:46:38] WARNING: no name column found on line 194 212: [20:46:38] WARNING: no name column found on line 195 212: [20:46:38] WARNING: no name column found on line 196 212: [20:46:38] WARNING: no name column found on line 197 212: [20:46:38] WARNING: no name column found on line 198 212: [20:46:38] WARNING: no name column found on line 199 212: [20:46:38] WARNING: no name column found on line 200 212: [20:46:38] WARNING: no name column found on line 201 212: [20:46:38] WARNING: no name column found on line 202 212: [20:46:38] WARNING: no name column found on line 203 212: [20:46:38] WARNING: no name column found on line 204 212: [20:46:38] WARNING: no name column found on line 205 212: [20:46:38] WARNING: no name column found on line 206 212: [20:46:38] WARNING: no name column found on line 207 212: [20:46:38] WARNING: no name column found on line 208 212: [20:46:38] WARNING: no name column found on line 209 212: [20:46:38] WARNING: no name column found on line 210 212: [20:46:38] WARNING: no name column found on line 211 212: [20:46:38] WARNING: no name column found on line 212 212: [20:46:38] WARNING: no name column found on line 213 212: [20:46:38] WARNING: no name column found on line 214 212: [20:46:38] WARNING: no name column found on line 215 212: [20:46:38] WARNING: no name column found on line 216 212: ...... 212: ---------------------------------------------------------------------- 212: Ran 10 tests in 2.664s 212: 212: OK 212: .................. 212: ---------------------------------------------------------------------- 212: Ran 18 tests in 11.089s 212: 212: OK 212: ... 212: ---------------------------------------------------------------------- 212: Ran 3 tests in 1.257s 212: 212: OK 212: ........ 212: ---------------------------------------------------------------------- 212: Ran 8 tests in 0.368s 212: 212: OK 212: .. 212: ---------------------------------------------------------------------- 212: Ran 2 tests in 0.295s 212: 212: OK 212: .. 212: ---------------------------------------------------------------------- 212: Ran 2 tests in 0.294s 212: 212: OK 212: . 212: ---------------------------------------------------------------------- 212: Ran 1 test in 0.890s 212: 212: OK 212: ........ 212: ---------------------------------------------------------------------- 212: Ran 8 tests in 0.014s 212: 212: OK 212: ... 212: ---------------------------------------------------------------------- 212: Ran 3 tests in 0.025s 212: 212: OK 212: ... 212: ---------------------------------------------------------------------- 212: Ran 3 tests in 0.022s 212: 212: OK 212: .... 212: ---------------------------------------------------------------------- 212: Ran 4 tests in 0.028s 212: 212: OK 212: ....... 212: ---------------------------------------------------------------------- 212: Ran 7 tests in 0.270s 212: 212: OK 212: .... 212: ---------------------------------------------------------------------- 212: Ran 4 tests in 0.313s 212: 212: OK 212: .... 212: ---------------------------------------------------------------------- 212: Ran 4 tests in 51.958s 212: 212: OK 212: .......... 212: ---------------------------------------------------------------------- 212: Ran 10 tests in 1.153s 212: 212: OK 212: . 212: ---------------------------------------------------------------------- 212: Ran 1 test in 0.012s 212: 212: OK 212: .......... 212: ---------------------------------------------------------------------- 212: Ran 10 tests in 0.081s 212: 212: OK 212: ..../home/farah/anaconda3/lib/python3.9/site-packages/rdkit/Chem/Randomize.py:29: DeprecationWarning: The random parameter to shuffle() has been deprecated 212: since Python 3.9 and will be removed in a subsequent version. 212: random.shuffle(order, random=random.random) 212: . 212: ---------------------------------------------------------------------- 212: Ran 5 tests in 1.876s 212: 212: OK 212: ................[20:50:30] Molecule does not have explicit Hs. Consider calling AddHs() 212: [20:50:30] Molecule does not have explicit Hs. Consider calling AddHs() 212: ..... 212: ---------------------------------------------------------------------- 212: Ran 21 tests in 83.367s 212: 212: OK 212: mol_197 212: 219.10,35.89,110.98,11.56,110.32,11.04,95.23,10.25,0.00 212: mol_223 212: 243.69,7.30,134.82,1.04,134.75,1.04,85.57,0.33,0.00 212: mol_269 212: 216.26,5.67,105.00,0.87,103.81,0.89,89.27,0.92,6.00 212: . 212: ---------------------------------------------------------------------- 212: Ran 1 test in 0.005s 212: 212: OK 212: ...[20:50:36] 212: 212: 212: Pre-condition Violation 212: molecule has no conformers 212: Violation occurred on line 37 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp 212: Failed Expression: dp_mol->getNumConformers() 212: 212: 212: . 212: ---------------------------------------------------------------------- 212: Ran 4 tests in 0.406s 212: 212: OK 1/1 Test #212: pythonTestDirChem ................***Timeout 1500.17 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 1500.47 sec

The following tests FAILED: 212 - pythonTestDirChem (Timeout)

Help me in removing these failures

[lnicco]

wrong repository?

[Rumeza]

No, repository is not wrong

[afrind]

This repo is for the mvfst QUIC library. We don't own these python tests.

Can you give the command to reproduce this error and details about your system?

[Rumeza]

Oh i mistakenly posted it here. Sorry for inconvenience