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Compatibility with Python-3.12 #6499

Open
Tracked by #156
, #8
...
sagitter opened this issue Jun 27, 2023 · 1 comment
Open
Tracked by #156
, #8
...

Compatibility with Python-3.12 #6499

sagitter opened this issue Jun 27, 2023 · 1 comment
Labels
bug

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@sagitter
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sagitter commented Jun 27, 2023 •
edited

Hi all.

Describe the bug
Some tests are failing when Python-3.12 is used; please, fix them if possible.

To Reproduce
Compiling RDKIT-2023.3.2 with Python-3.12.0~b3

Configuration (please complete the following information):

  • RDKit version: 2023.3.2
  • OS: Fedora 39
  • Python version: Python-3.12.0~b3

Additional context
Ouput log:

+ export LD_LIBRARY_PATH=/builddir/build/BUILDROOT/rdkit-2023.03.2-1.fc39.x86_64/usr/lib64
+ LD_LIBRARY_PATH=/builddir/build/BUILDROOT/rdkit-2023.03.2-1.fc39.x86_64/usr/lib64
+ export PYTHONPATH=/builddir/build/BUILDROOT/rdkit-2023.03.2-1.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/rdkit-2023.03.2-1.fc39.x86_64/usr/lib64/python3.12/site-packages
+ export RDBASE=/builddir/build/BUILD/rdkit-Release_2023_03_2
+ RDBASE=/builddir/build/BUILD/rdkit-Release_2023_03_2
+ /usr/bin/ctest --test-dir . --output-on-failure --force-new-ctest-process -j6 -- -E 'pythonTestSping|pythonTestDirChem|testPgSQL'
Test project /builddir/build/BUILD/rdkit-Release_2023_03_2
...
 75/197 Test  #80: pyChemReactions ........................***Failed    0.36 sec
[18:17:28] 
****
Pre-condition Violation
getNumImplicitHs() called without preceding call to calcImplicitValence()
Violation occurred on line 297 in file /builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/Atom.cpp
Failed Expression: d_implicitValence > -1
****
[18:17:28] 
****
Pre-condition Violation
getNumImplicitHs() called without preceding call to calcImplicitValence()
Violation occurred on line 297 in file /builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/Atom.cpp
Failed Expression: d_implicitValence > -1
****
.....[18:17:28] stereo atoms in input cannot be mapped to output (atoms are no longer bonded)
[18:17:28] stereo atoms in input cannot be mapped to output (atoms are no longer bonded)
[18:17:28] stereo atoms in input cannot be mapped to output (atoms are no longer bonded)
[18:17:28] stereo atoms in input cannot be mapped to output (atoms are no longer bonded)
.[18:17:28] product atom-mapping number 1 found multiple times.
[18:17:28] product atom-mapping number 1 found multiple times.
................[18:17:28] mapped atoms in the reactants were not mapped in the products.
  unmapped numbers are: 3 
[18:17:28] mapped atoms in the reactants were not mapped in the products.
  unmapped numbers are: 3 
.[18:17:28] mapped atoms in the reactants were not mapped in the products.
  unmapped numbers are: 3 
..E.EEE...[18:17:28] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q
[18:17:28] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q'
[18:17:28] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q
[18:17:28] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q'
.[18:17:28] reactant atom-mapping number 1 found multiple times.
[18:17:28] product atom-mapping number 2 not found in reactants.
[18:17:28] mapped atoms in the reactants were not mapped in the products.
  unmapped numbers are: 4 
[18:17:28] product atom-mapping number 5 not found in reactants.
......EE.E.[18:17:28] SMARTS Parse Error: syntax error while parsing: boromicacid
[18:17:28] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid'
[18:17:28] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide
[18:17:28] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide'
[18:17:28] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride
[18:17:28] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride'
[18:17:28] reaction has no reactants
[18:17:28] reaction has no products
[18:17:28] initialization failed
[18:17:28] reaction has no reactants
[18:17:28] reaction has no products
.[18:17:28] SMARTS Parse Error: syntax error while parsing: boromicacid
[18:17:28] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid'
[18:17:28] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide
[18:17:28] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide'
[18:17:28] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride
[18:17:28] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride'
[18:17:28] reaction has no reactants
[18:17:28] reaction has no products
[18:17:28] initialization failed
[18:17:28] reaction has no reactants
[18:17:28] reaction has no products
.
======================================================================
ERROR: test19RemoveUnmappedMoleculesToAgents (__main__.TestCase.test19RemoveUnmappedMoleculesToAgents)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 512, in test19RemoveUnmappedMoleculesToAgents
    self.failUnless(rxn)
    ^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'failUnless'
======================================================================
ERROR: test20CheckCopyConstructedReactionAtomProps (__main__.TestCase.test20CheckCopyConstructedReactionAtomProps)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 555, in test20CheckCopyConstructedReactionAtomProps
    self.assertEquals(res, res2)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: test21CheckRawIters (__main__.TestCase.test21CheckRawIters)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 565, in test21CheckRawIters
    self.assertEquals(len(reactants), rxn.GetNumReactantTemplates())
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: test22RunSingleReactant (__main__.TestCase.test22RunSingleReactant)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 630, in test22RunSingleReactant
    self.assertEquals(result, expected_result)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testPreprocess (__main__.TestCase.testPreprocess)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 688, in testPreprocess
    self.assertEquals(res,
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testProperties (__main__.TestCase.testProperties)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 699, in testProperties
    self.assertEquals(rxn.GetIntProp("intprop"), 3)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: test_PNGMetadata (__main__.TestCase.test_PNGMetadata)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 736, in test_PNGMetadata
    self.failIf(rxn is None)
    ^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'failIf'. Did you mean: 'fail'?
----------------------------------------------------------------------
Ran 47 tests in 0.096s
FAILED (errors=7)
********************************************
/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/testData/AmideBond.rxn
<rdkit.Chem.rdChemReactions.ChemicalReaction object at 0x7f6c5888f140>
        Start  81: pyChemReactionEnumerations
 76/197 Test  #59: fileParsersTest1 .......................   Passed    4.35 sec
        Start  82: pyChemReactionSanitize
 77/197 Test  #81: pyChemReactionEnumerations .............***Failed    1.30 sec
[18:17:28] == testCartesianProduct
E[18:17:28] == testEnumerateLibrary
EE[18:17:28] == testRGroupState
E[18:17:28] == testRandomEnumerateAllBBsLibrary
** [1, 1]
** [0, 2]
E[18:17:28] == testRandomEnumerateLibrary
E[18:17:28] == testRandomSample
E[18:17:28] == testRandomSampleAllBBs
E[18:17:28]  deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead
[18:17:28]  deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead
.[18:17:28] == testRemoveBadMatches
E[18:17:28] == testTimings
.
======================================================================
ERROR: testCartesianProduct (__main__.TestCase.testCartesianProduct)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py", line 63, in testCartesianProduct
    self.assertEquals(cartProd.GetNumPermutations(), 10 * 5 * 6)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testEnumerateLibrary (__main__.TestCase.testEnumerateLibrary)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py", line 241, in testEnumerateLibrary
    self.assertEquals(rxn.ToBinary(), enumerator.GetReaction().ToBinary())
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testEvenPairsSampling (__main__.TestCase.testEvenPairsSampling)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py", line 174, in testEvenPairsSampling
    self.assertEquals(np.median(list(pairs01.values())), 1.0)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testRGroupState (__main__.TestCase.testRGroupState)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py", line 510, in testRGroupState
    self.assertEquals(tostr(enumerator.nextSmiles()), tostr(p))
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testRandomEnumerateAllBBsLibrary (__main__.TestCase.testRandomEnumerateAllBBsLibrary)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py", line 425, in testRandomEnumerateAllBBsLibrary
    self.assertEquals(r1, set([0, 1]))  # two bbs at reagent one all sampled at one iteration
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testRandomEnumerateLibrary (__main__.TestCase.testRandomEnumerateLibrary)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py", line 362, in testRandomEnumerateLibrary
    self.assertEquals(enumerator.GetEnumerator().Type(), enumerator2.GetEnumerator().Type())
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testRandomSample (__main__.TestCase.testRandomSample)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py", line 87, in testRandomSample
    self.assertEquals(randProd.GetNumPermutations(), 10 * 5 * 6)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testRandomSampleAllBBs (__main__.TestCase.testRandomSampleAllBBs)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py", line 112, in testRandomSampleAllBBs
    self.assertEquals(randProd.GetNumPermutations(), 10 * 5 * 6)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testRemovingBadMatches (__main__.TestCase.testRemovingBadMatches)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py", line 571, in testRemovingBadMatches
    self.assertEquals([], list(enumerator))
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
----------------------------------------------------------------------
Ran 11 tests in 1.001s
FAILED (errors=9)
<rdkit.Chem.rdChemReactions.CartesianProductStrategy object at 0x7f113d7443b0> Skipped 10000000 in 0.04132342338562012 seconds
<rdkit.Chem.rdChemReactions.RandomSampleStrategy object at 0x7f113d744220> Skipped 10000000 in 0.4523501396179199 seconds
<rdkit.Chem.rdChemReactions.RandomSampleAllBBsStrategy object at 0x7f113d744450> Skipped 10000000 in 0.3625645637512207 seconds
        Start  83: testChemTransforms
 78/197 Test  #83: testChemTransforms .....................   Passed    0.05 sec
        Start  84: chemTransformsTestCatch
 79/197 Test  #82: pyChemReactionSanitize .................***Failed    0.34 sec
.[18:17:29] reactant 0 has no mapped atoms.
[18:17:29] product 0 has no mapped atoms.
[18:17:29] reactant 0 has no mapped atoms.
[18:17:29] product 0 has no mapped atoms.
.E.
======================================================================
ERROR: test_sanitize (__main__.TestCase.test_sanitize)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ChemReactions/Wrap/testSanitize.py", line 287, in test_sanitize
    self.assertEquals(res, good_res)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
----------------------------------------------------------------------
Ran 4 tests in 0.013s
FAILED (errors=1)
()
********************************************
$RXN
      RDKit
  2  1
$MOL
     RDKit          2D
  2  1  0  0  0  0  0  0  0  0999 V2000
   -3.2730   -7.0542    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
   -3.9875   -7.4667    0.0000 R#  0  0  0  0  0  0  0  0  0  1  0  0
  1  2  1  0
M  RGP  1   2   1
V    1 halogen.bromine.aromatic
V    2 [*:1]
M  END
$MOL
     RDKit          2D
  4  3  0  0  0  0  0  0  0  0999 V2000
    3.4375   -7.7917    0.0000 R#  0  0  0  0  0  0  0  0  0  2  0  0
    4.1520   -7.3792    0.0000 B   0  0  0  0  0  0  0  0  0  0  0  0
    4.1520   -6.5542    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8664   -7.7917    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0
  1  2  1  0
  2  4  1  0
M  RGP  1   1   2
V    1 [*:2]
V    2 boronicacid
M  END
$MOL
     RDKit          2D
  2  1  0  0  0  0  0  0  0  0999 V2000
   11.2667   -7.3417    0.0000 R#  0  0  0  0  0  0  0  0  0  1  0  0
   11.9811   -6.9292    0.0000 R#  0  0  0  0  0  0  0  0  0  2  0  0
  1  2  1  0
M  RGP  2   1   1   2   2
V    1 [*:1]
V    2 [*:2]
M  END
      ...
        Start  93: pyFragCatalog
 88/197 Test  #91: pyFilterCatalog ........................***Failed    0.37 sec
..E...EEE.EE.[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
[18:17:30] SMILES Parse Error: syntax error while parsing: ---
[18:17:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
[18:17:30] dasfsadf
.EE.....
======================================================================
ERROR: test2FilterCatalogTest (__main__.TestCase.test2FilterCatalogTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/FilterCatalog/Wrap/rough_test.py", line 172, in test2FilterCatalogTest
    self.assertEquals(entry.GetProp(key), "PAINS_A")
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testFilterHierarchyMatcher (__main__.TestCase.testFilterHierarchyMatcher)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/FilterCatalog/Wrap/rough_test.py", line 376, in testFilterHierarchyMatcher
    root.AddChild(hierarchy(sm))
                  ^^^^^^^^^^^^^
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/FilterCatalog/Wrap/rough_test.py", line 372, in hierarchy
    self.assertEquals(matcher.GetName(), node.GetName())
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testFlattenedFunctionalGroupHierarchy (__main__.TestCase.testFlattenedFunctionalGroupHierarchy)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/FilterCatalog/Wrap/rough_test.py", line 500, in testFlattenedFunctionalGroupHierarchy
    self.assertEquals(hits, res)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testFunctionalGroupHierarchy (__main__.TestCase.testFunctionalGroupHierarchy)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/FilterCatalog/Wrap/rough_test.py", line 471, in testFunctionalGroupHierarchy
    self.assertEquals(res, hits)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testPyFilter (__main__.TestCase.testPyFilter)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/FilterCatalog/Wrap/rough_test.py", line 312, in testPyFilter
    self.assertEquals(func.GetName(), "FilterMatcher")
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testRemoveEntry (__main__.TestCase.testRemoveEntry)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/FilterCatalog/Wrap/rough_test.py", line 292, in testRemoveEntry
    self.assertEquals(count, newcount + 1)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testThreadedRunner (__main__.TestCase.testThreadedRunner)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/FilterCatalog/Wrap/rough_test.py", line 530, in testThreadedRunner
    self.assertEquals(len(smiles), 3)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
======================================================================
ERROR: testZinc (__main__.TestCase.testZinc)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/FilterCatalog/Wrap/rough_test.py", line 241, in testZinc
    self.assertEquals(catalog.GetFirstMatch(m), None)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
----------------------------------------------------------------------
Ran 21 tests in 0.089s
FAILED (errors=8)
(Five aromatic carbons And (Not any of Five aromatic carbons))
(Five aromatic carbons Or (Not any of Five aromatic carbons))
(Not (Five aromatic carbons And (Not any of Five aromatic carbons)))
********************************************
Testing: PAINS_A 2
Count 1
********************************************
{'Cl,Br,I'}
1
2
running
  ...
        Start 125: pyChemicalFeatures
120/197 Test #125: pyChemicalFeatures .....................***Failed    1.02 sec
EE[18:17:58] Molecule does not have explicit Hs. Consider calling AddHs()
..E[18:17:58] Molecule does not have explicit Hs. Consider calling AddHs()
.EEE
======================================================================
ERROR: testAtomMatch (__main__.TestCase.testAtomMatch)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py", line 153, in testAtomMatch
    self.failUnless(cfac.GetNumFeatureDefs() == 2)
    ^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'failUnless'
======================================================================
ERROR: testBasic (__main__.TestCase.testBasic)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py", line 30, in testBasic
    self.failUnless(cfac.GetNumFeatureDefs() == 2)
    ^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'failUnless'
======================================================================
ERROR: testIncludeOnly (__main__.TestCase.testIncludeOnly)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py", line 71, in testIncludeOnly
    self.failUnless(cfac.GetNumFeatureDefs() == 2)
    ^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'failUnless'
======================================================================
ERROR: testParseErrorHandling (__main__.TestCase.testParseErrorHandling)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py", line 128, in testParseErrorHandling
    self.failUnlessRaises(ValueError,
    ^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'failUnlessRaises'
======================================================================
ERROR: testStringParse (__main__.TestCase.testStringParse)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py", line 105, in testStringParse
    self.failUnless(cfac.GetNumFeatureDefs() == 2)
    ^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'failUnless'
======================================================================
ERROR: testStringParse2 (__main__.TestCase.testStringParse2)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py", line 119, in testStringParse2
    self.failUnless(cfac.GetNumFeatureDefs() == 2)
    ^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'failUnless'
----------------------------------------------------------------------
Ran 9 tests in 0.290s
FAILED (errors=6)
     ...
        Start 157: pySLNParse
152/197 Test #157: pySLNParse .............................***Failed    1.31 sec
EE
======================================================================
ERROR: test1Basics (__main__.TestCase.test1Basics)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/SLNParse/Wrap/testSLN.py", line 50, in test1Basics
    self.failUnless(m1)
    ^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'failUnless'
======================================================================
ERROR: test2Queries (__main__.TestCase.test2Queries)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/SLNParse/Wrap/testSLN.py", line 59, in test2Queries
    self.failUnless(patt)
    ^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'failUnless'
----------------------------------------------------------------------
Ran 2 tests in 0.063s
FAILED (errors=2)
       ...
        Start 189: testChemicalFeatures
184/197 Test #188: pyRanker ...............................***Failed    0.32 sec
..E..
======================================================================
ERROR: test2ranker (__main__.TestCase.test2ranker)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/ML/InfoTheory/Wrap/testRanker.py", line 123, in test2ranker
    with self.assertRaisesRegexp(Exception, ""):
         ^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertRaisesRegexp'. Did you mean: 'assertRaisesRegex'?
----------------------------------------------------------------------
Ran 5 tests in 0.022s
FAILED (errors=1)
      ...
        Start 194: pythonTestDirDataStructs
189/197 Test #158: pyGraphMolWrap .........................***Failed   14.00 sec
..............[18:18:37] SMARTS Parse Error: syntax error while parsing: fiib
[18:18:37] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib'
....[18:18:37] ERROR: Problems encountered parsing data fields
[18:18:37] ERROR: moving to the beginning of the next molecule
[18:18:37] ERROR: Problems encountered parsing data fields
[18:18:37] ERROR: moving to the beginning of the next molecule
[18:18:37] Spurious data before the first property will be ignored
[18:18:37] Property <ID> will be truncated after the first blank line
[18:18:37] Property <ID> will be truncated after the first blank line
[18:18:37] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
[18:18:37] ERROR: Problems encountered parsing data fields
[18:18:37] ERROR: moving to the beginning of the next molecule
[18:18:37] ERROR: Problems encountered parsing data fields
[18:18:37] ERROR: moving to the beginning of the next molecule
[18:18:37] Spurious data before the first property will be ignored
[18:18:37] Property <ID> will be truncated after the first blank line
[18:18:37] Property <ID> will be truncated after the first blank line
[18:18:37] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
[18:18:37] ERROR: Problems encountered parsing data fields
[18:18:37] ERROR: moving to the beginning of the next molecule
[18:18:37] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
[18:18:37] ERROR: Problems encountered parsing data fields
[18:18:37] ERROR: moving to the beginning of the next molecule
[18:18:37] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
.[18:18:37] SMILES Parse Error: syntax error while parsing: fail
[18:18:37] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail'
[18:18:37] ERROR: Smiles parse error on line 2
[18:18:37] ERROR: Cannot create molecule from : 'fail'
>>> This may result in an infinite loop.  It should finish almost instantly
<<< OK, it finished.
............[18:18:37] Explicit valence for atom # 1 C, 5, is greater than permitted
..........E.[18:18:37] non-ring atom 0 marked aromatic
[18:18:37] non-ring atom 0 marked aromatic
[18:18:37] 
****
Range Error
idx
Violation occurred on line 213 in file /builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ROMol.cpp
Failed Expression: 12 < 6
****
[18:18:37] non-ring atom 0 marked aromatic
[18:18:37] non-ring atom 0 marked aromatic
[18:18:37] 
****
Range Error
idx
Violation occurred on line 213 in file /builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ROMol.cpp
Failed Expression: 12 < 6
****
...............[18:18:37] 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.
[18:18:37] 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.
..............[18:18:37] Can't kekulize mol.  Unkekulized atoms: 0 1 2 3 4
[18:18:37] Explicit valence for atom # 1 C, 5, is greater than permitted
...........................[18:18:41]  unable to set wavy bonds for double bonds: 3
.........[18:18:41] 
****
Range Error
idx
Violation occurred on line 213 in file /builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ROMol.cpp
Failed Expression: 6 < 5
****
...................[18:18:42] Explicit valence for atom # 1 F, 2, is greater than permitted
[18:18:42] Explicit valence for atom # 6 F, 2, is greater than permitted
[18:18:42] Can't kekulize mol.  Unkekulized atoms: 3 4 5
.[18:18:42] Warning: molecule is tagged as 3D, but all Z coords are zero
[18:18:42] Warning: molecule is tagged as 3D, but all Z coords are zero
[18:18:42] Warning: molecule is tagged as 3D, but all Z coords are zero
[18:18:42] Warning: molecule is tagged as 3D, but all Z coords are zero
[18:18:42] Warning: molecule is tagged as 3D, but all Z coords are zero
[18:18:42] Warning: molecule is tagged as 3D, but all Z coords are zero
...............[18:18:49] 
****
Pre-condition Violation
no owner
Violation occurred on line 138 in file /builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/Atom.h
Failed Expression: dp_mol
****
[18:18:49] 
****
Pre-condition Violation
no owner
Violation occurred on line 138 in file /builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/Atom.h
Failed Expression: dp_mol
****
[18:18:49] 
****
Pre-condition Violation
no owner
Violation occurred on line 138 in file /builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/Atom.h
Failed Expression: dp_mol
****
[18:18:49] 
****
Pre-condition Violation
no owner
Violation occurred on line 138 in file /builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/Atom.h
Failed Expression: dp_mol
****
[18:18:49] 
****
Pre-condition Violation
no owner
Violation occurred on line 138 in file /builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/Atom.h
Failed Expression: dp_mol
****
.....[18:18:49] 
****
Range Error
atomIdx1
Violation occurred on line 375 in file /builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/RWMol.cpp
Failed Expression: 0 < 0
****
......[18:18:49] SMILES Parse Error: unclosed ring for input: 'c1ccccc'
[18:18:49] ERROR: Smiles parse error on line 0
[18:18:49] ERROR: Cannot create molecule from : 'c1ccccc'
[18:18:49] SMILES Parse Error: extra open parentheses for input: 'C(C'
[18:18:49] ERROR: Smiles parse error on line 3
[18:18:49] ERROR: Cannot create molecule from : 'C(C'
[18:18:49] Explicit valence for atom # 1 C, 5, is greater than permitted
[18:18:49] ERROR: Could not sanitize molecule on line 6
[18:18:49] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted
[18:18:49] SMILES Parse Error: unclosed ring for input: 'c1ccccc'
[18:18:49] ERROR: Smiles parse error on line 0
[18:18:49] ERROR: Cannot create molecule from : 'c1ccccc'
[18:18:49] SMILES Parse Error: extra open parentheses for input: 'C(C'
[18:18:49] ERROR: Smiles parse error on line 3
[18:18:49] ERROR: Cannot create molecule from : 'C(C'
[18:18:49] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC'
[18:18:49] ERROR: Smiles parse error on line 6
[18:18:49] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC'
[18:18:49] Explicit valence for atom # 1 F, 2, is greater than permitted
[18:18:49] ERROR: Could not sanitize molecule ending on line 21
[18:18:49] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted
[18:18:49] ERROR: EOF hit while reading atoms
[18:18:49] ERROR: moving to the beginning of the next molecule
[18:18:49] Explicit valence for atom # 1 F, 2, is greater than permitted
[18:18:49] ERROR: Could not sanitize molecule ending on line 21
[18:18:49] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted
[18:18:49] ERROR: EOF hit while reading atoms
[18:18:49] ERROR: moving to the beginning of the next molecule
....[18:18:49] 
****
Pre-condition Violation
RingInfo not initialized
Violation occurred on line 169 in file /builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/RingInfo.cpp
Failed Expression: df_init
****
........[18:18:49] 
****
Range Error
idx
Violation occurred on line 213 in file /builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/ROMol.cpp
Failed Expression: 3 < 1
****
..[18:18:49] Can't kekulize mol.  Unkekulized atoms: 0 1 2 3 4
........................[18:18:49] SMILES Parse Error: unclosed ring for input: 'C1CC'
......[18:18:49] WARNING: not removing hydrogen atom without neighbors
[18:18:49] WARNING: not removing hydrogen atom with dummy atom neighbors
[18:18:49] WARNING: not removing hydrogen atom with wedged bond
[18:18:49] WARNING: not removing hydrogen atom without neighbors
[18:18:49] WARNING: not removing hydrogen atom with dummy atom neighbors
.....[18:18:49] Explicit valence for atom # 1 F, 2, is greater than permitted
[18:18:49] Can't kekulize mol.  Unkekulized atoms: 0 1 2
.[18:18:49] Explicit valence for atom # 1 F, 2, is greater than permitted
[18:18:49] Explicit valence for atom # 1 F, 2, is greater than permitted
[18:18:49] Explicit valence for atom # 1 F, 2, is greater than permitted
[18:18:49] Explicit valence for atom # 1 F, 2, is greater than permitted
[18:18:49] Can't kekulize mol.  Unkekulized atoms: 0 1 2
[18:18:49] Can't kekulize mol.  Unkekulized atoms: 0 1 2
[18:18:49] Can't kekulize mol.  Unkekulized atoms: 0 1 2
..........[18:18:49] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname
[18:18:49] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname'
.[18:18:49] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname
[18:18:49] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname'
..[18:18:49] SMILES Parse Error: syntax error while parsing: error
[18:18:49] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error'
[18:18:49] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd'
[18:18:49] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error'
[18:18:49] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd'
..............[18:18:49] SMILES Parse Error: syntax error while parsing: garbage_0
[18:18:49] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0'
[18:18:49] SMILES Parse Error: syntax error while parsing: garbage_2
[18:18:49] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2'
[18:18:49] SMILES Parse Error: syntax error while parsing: garbage_4
[18:18:49] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4'
..........
======================================================================
ERROR: test45RingInfo (__main__.TestCase.test45RingInfo)
test the RingInfo class
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/Code/GraphMol/Wrap/rough_test.py", line 2163, in test45RingInfo
    self.assertEquals(ri.NumRings(), 2)
    ^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
----------------------------------------------------------------------
Ran 241 tests in 12.517s
FAILED (errors=1)
643
supplier: <class 'rdkit.Chem.rdmolfiles.SmilesMolSupplier'>
supplier: <class 'rdkit.Chem.rdmolfiles.SDMolSupplier'>
supplier: <class 'rdkit.Chem.rdmolfiles.TDTMolSupplier'>
        Start 195: pythonTestDirDbase
190/197 Test #195: pythonTestDirDbase .....................***Failed    0.96 sec
..
----------------------------------------------------------------------
Ran 2 tests in 0.031s
OK
...........
----------------------------------------------------------------------
Ran 11 tests in 0.097s
OK
.
----------------------------------------------------------------------
Ran 1 test in 0.001s
OK
FFEEEEE.F......
======================================================================
ERROR: testGetData1 (__main__.TestCase.testGetData1)
basic functionality
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 96, in testGetData1
    with self.assertRaisesRegexp(IndexError, ""):
         ^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertRaisesRegexp'. Did you mean: 'assertRaisesRegex'?
======================================================================
ERROR: testGetData2 (__main__.TestCase.testGetData2)
using a RandomAccessDbResultSet
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 106, in testGetData2
    with self.assertRaisesRegexp(IndexError, ""):
         ^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertRaisesRegexp'. Did you mean: 'assertRaisesRegex'?
======================================================================
ERROR: testGetData3 (__main__.TestCase.testGetData3)
using a DbResultSet
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 113, in testGetData3
    with self.assertRaisesRegexp(TypeError, ""):
         ^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertRaisesRegexp'. Did you mean: 'assertRaisesRegex'?
======================================================================
ERROR: testGetData4 (__main__.TestCase.testGetData4)
using a RandomAccessDbResultSet with a Transform
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 133, in testGetData4
    with self.assertRaisesRegexp(IndexError, ""):
         ^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertRaisesRegexp'. Did you mean: 'assertRaisesRegex'?
======================================================================
ERROR: testGetData5 (__main__.TestCase.testGetData5)
using a DbResultSet with a Transform
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 144, in testGetData5
    with self.assertRaisesRegexp(TypeError, ""):
         ^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'TestCase' object has no attribute 'assertRaisesRegexp'. Did you mean: 'assertRaisesRegex'?
======================================================================
FAIL: test1Txt (__main__.TestCase.test1Txt)
test reading from a text file
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 77, in test1Txt
    self._confirm(tblName, dbName=self.tempDbName)
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm
    assert len(res) == len(colHeads), 'bad number of columns'
AssertionError: bad number of columns
======================================================================
FAIL: test3Txt (__main__.TestCase.test3Txt)
test reading from a text file including null markers
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 87, in test3Txt
    self._confirm(tblName, dbName=self.tempDbName)
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm
    assert len(res) == len(colHeads), 'bad number of columns'
AssertionError: bad number of columns
======================================================================
FAIL: test_DatabaseToDatabase (__main__.TestCase.test_DatabaseToDatabase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 219, in test_DatabaseToDatabase
    self._confirm(tblName, dbName=self.tempDbName, colHeads=['id', 'val'])
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm
    assert len(res) == len(colHeads), 'bad number of columns'
AssertionError: bad number of columns
----------------------------------------------------------------------
Ran 15 tests in 0.049s
FAILED (failures=3, errors=5)
......
----------------------------------------------------------------------
Ran 6 tests in 0.003s
OK
!!! TEST FAILURE:  python UnitTestDbUtils.py {}
        Start 196: pythonTestDirSimDivFilters
191/197 Test #196: pythonTestDirSimDivFilters .............   Passed    0.65 sec
        Start 197: pythonTestDirVLib
192/197 Test #194: pythonTestDirDataStructs ...............***Failed    1.86 sec
.......
----------------------------------------------------------------------
Ran 7 tests in 0.041s
OK
..............E................E..
======================================================================
ERROR: testSparseIdx (__main__.ExplicitTestCase.testSparseIdx)
test indexing into SparseBitVects
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/DataStructs/UnitTestcBitVect.py", line 41, in testSparseIdx
    with self.assertRaisesRegexp(IndexError, ""):
         ^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'ExplicitTestCase' object has no attribute 'assertRaisesRegexp'. Did you mean: 'assertRaisesRegex'?
======================================================================
ERROR: testSparseIdx (__main__.SparseBitVectTests.testSparseIdx)
test indexing into SparseBitVects
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/DataStructs/UnitTestcBitVect.py", line 41, in testSparseIdx
    with self.assertRaisesRegexp(IndexError, ""):
         ^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'SparseBitVectTests' object has no attribute 'assertRaisesRegexp'. Did you mean: 'assertRaisesRegex'?
----------------------------------------------------------------------
Ran 34 tests in 0.010s
FAILED (errors=2)
.....
----------------------------------------------------------------------
Ran 5 tests in 0.020s
OK
.......
----------------------------------------------------------------------
Ran 7 tests in 0.001s
OK
!!! TEST FAILURE:  python UnitTestcBitVect.py {}
193/197 Test #197: pythonTestDirVLib ......................   Passed    0.62 sec
194/197 Test #193: pythonTestDirML ........................   Passed   14.53 sec
195/197 Test #191: pythonTestDbCLI ........................   Passed   16.81 sec
196/197 Test   #4: testConcurrentQueue ....................   Passed  114.12 sec
197/197 Test #117: testDistGeomHelpers ....................   Passed  113.24 sec
95% tests passed, 10 tests failed out of 197
Total Test time (real) = 133.67 sec
The following tests FAILED:
	 80 - pyChemReactions (Failed)
	 81 - pyChemReactionEnumerations (Failed)
	 82 - pyChemReactionSanitize (Failed)
	 91 - pyFilterCatalog (Failed)
	125 - pyChemicalFeatures (Failed)
	157 - pySLNParse (Failed)
	158 - pyGraphMolWrap (Failed)
	188 - pyRanker (Failed)
	194 - pythonTestDirDataStructs (Failed)
	195 - pythonTestDirDbase (Failed)
Errors while running CTest
@sagitter sagitter added the bug label Jun 27, 2023
ptosco pushed a commit to ptosco/rdkit that referenced this issue Jun 27, 2023
fixes rdkit#6499
83c18e5
@ptosco ptosco linked a pull request Jun 27, 2023 that will close this issue
fixes #6499 #6500
Closed
@sagitter
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Thank you very much Paolo.

Just one test is still failing:

190/197 Test #195: pythonTestDirDbase .....................***Failed    0.87 sec
..
----------------------------------------------------------------------
Ran 2 tests in 0.015s
OK
...........
----------------------------------------------------------------------
Ran 11 tests in 0.032s
OK
.
----------------------------------------------------------------------
Ran 1 test in 0.001s
OK
FF......F......
======================================================================
FAIL: test1Txt (__main__.TestCase.test1Txt)
test reading from a text file
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 77, in test1Txt
    self._confirm(tblName, dbName=self.tempDbName)
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm
    assert len(res) == len(colHeads), 'bad number of columns'
AssertionError: bad number of columns
======================================================================
FAIL: test3Txt (__main__.TestCase.test3Txt)
test reading from a text file including null markers
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 87, in test3Txt
    self._confirm(tblName, dbName=self.tempDbName)
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm
    assert len(res) == len(colHeads), 'bad number of columns'
AssertionError: bad number of columns
======================================================================
FAIL: test_DatabaseToDatabase (__main__.TestCase.test_DatabaseToDatabase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 219, in test_DatabaseToDatabase
    self._confirm(tblName, dbName=self.tempDbName, colHeads=['id', 'val'])
  File "/builddir/build/BUILD/rdkit-Release_2023_03_2/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm
    assert len(res) == len(colHeads), 'bad number of columns'
AssertionError: bad number of columns
----------------------------------------------------------------------
Ran 15 tests in 0.032s
FAILED (failures=3)
......
----------------------------------------------------------------------
Ran 6 tests in 0.003s
OK
!!! TEST FAILURE:  python UnitTestDbUtils.py {}

@davidegraff davidegraff mentioned this issue Oct 6, 2023
Closed
1 task
This was referenced Oct 11, 2023
Merged
Merged
Closed
@JacksonBurns JacksonBurns mentioned this issue Oct 26, 2023
Closed
1 task
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fixes #6499 ptosco/rdkit
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