Dear colleagues,
after compiling and installing last RDKit under Ubuntu12.04 (64bit) I have
following test failed.
The following tests FAILED:
3 - pyBV (Failed)
8 - testPyGeometry (Failed)
35 - pyChemReactions (Failed)
42 - pyMolDescriptors (Failed)
61 - pyGraphMolWrap (SEGFAULT)
69 - pyFeatures (Failed)
76 - pythonTestDirChem (Failed)
I can't find the source of mistakes and errors. Can you please suggest me
any solutions?
RDBASE is provided in .bashrc, boost and openbabel library are installed in
default Ubuntu paths.
Thank you,
--
Vladimir Chupakhin,
Boston, MA, USA
LinkedIN: http://www.linkedin.com/in/chupvl
*Info from the log file*
3/76 Testing: pyBV
3/76 Test: pyBV
Command: "/usr/bin/python"
"/home/chupvl/scisoft/rdkit/Code/DataStructs/Wrap/testBV.py"
Directory: /home/chupvl/scisoft/rdkit/build/Code/DataStructs/Wrap
"pyBV" start time: Aug 17 10:38 EDT
Output:
----------------------------------------------------------
.......EE
======================================================================
ERROR: test7FPS (__main__.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/chupvl/scisoft/rdkit/Code/DataStructs/Wrap/testBV.py", line
153, in test7FPS
self.failUnlessEqual(DataStructs.BitVectToFPSText(bv),"03008280")
AttributeError: 'module' object has no attribute 'BitVectToFPSText'
8/76 Testing: testPyGeometry
8/76 Test: testPyGeometry
Command: "/usr/bin/python"
"/home/chupvl/scisoft/rdkit/Code/Geometry/Wrap/testGeometry.py"
Directory: /home/chupvl/scisoft/rdkit/build/Code/Geometry/Wrap
"testPyGeometry" start time: Aug 17 10:38 EDT
Output:
----------------------------------------------------------
......E..
======================================================================
ERROR: test6Dihedrals (__main__.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/chupvl/scisoft/rdkit/Code/Geometry/Wrap/testGeometry.py",
line 350, in test6Dihedrals
ang = geom.ComputeDihedralAngle(p1,p2,p3,p4)
AttributeError: 'module' object has no attribute 'ComputeDihedralAngle'
----------------------------------------------------------------------
Ran 9 tests in 0.023s
FAILED (errors=1)
Testing Geometry wrapper
<end of output>
Test time = 0.08 sec
----------------------------------------------------------
Test Failed.
"testPyGeometry" end time: Aug 17 10:38 EDT
"testPyGeometry" time elapsed: 00:00:00
----------------------------------------------------------
35/76 Testing: pyChemReactions
35/76 Test: pyChemReactions
Command: "/usr/bin/python"
"/home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py"
Directory: /home/chupvl/scisoft/rdkit/build/Code/GraphMol/ChemReactions/Wrap
"pyChemReactions" start time: Aug 17 10:38 EDT
Output:
----------------------------------------------------------
......E...[10:38:56] SMARTS Parse Error: syntax error while parsing:
[C:1](=[O:2])Q
[10:38:56] SMARTS Parse Error: syntax error while parsing:
[C:1](=[O:2])[N:3]Q
.[10:38:56] reactant atom-mapping number 1 found multiple times.
[10:38:56] product atom-mapping number 2 not found in reactants.
F.E.
======================================================================
ERROR: test16GetReactingAtoms (__main__.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py",
line 399, in test16GetReactingAtoms
rAs = rxn.GetReactingAtoms()
AttributeError: 'ChemicalReaction' object has no attribute
'GetReactingAtoms'
======================================================================
ERROR: test8Properties (__main__.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py",
line 286, in test8Properties
self.failUnlessEqual(ps[0][0].GetAtomWithIdx(1).GetIsotope(),3);
AttributeError: 'Atom' object has no attribute 'GetIsotope'
======================================================================
FAIL: test5Validation (__main__.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/chupvl/scisoft/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py",
line 250, in test5Validation
self.failUnless(rxn.Validate()==(1,1))
AssertionError: False is not true
----------------------------------------------------------------------
Ran 15 tests in 0.008s
FAILED (failures=1, errors=2)
<end of output>
Test time = 0.10 sec
----------------------------------------------------------
Test Failed.
"pyChemReactions" end time: Aug 17 10:38 EDT
"pyChemReactions" time elapsed: 00:00:00
----------------------------------------------------------
42/76 Testing: pyMolDescriptors
42/76 Test: pyMolDescriptors
Command: "/usr/bin/python"
"/home/chupvl/scisoft/rdkit/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py"
Directory: /home/chupvl/scisoft/rdkit/build/Code/GraphMol/Descriptors/Wrap
"pyMolDescriptors" start time: Aug 17 10:38 EDT
Output:
----------------------------------------------------------
E...E..E.....
======================================================================
ERROR: testAtomPairOptions (__main__.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/chupvl/scisoft/rdkit/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py",
line 247, in testAtomPairOptions
fp1 = rdMD.GetAtomPairFingerprint(m1,atomInvariants=[1]*6)
ArgumentError: Python argument types in
rdkit.Chem.rdMolDescriptors.GetAtomPairFingerprint(Mol)
did not match C++ signature:
GetAtomPairFingerprint(RDKit::ROMol mol, unsigned int minLength=1,
unsigned int maxLength=30, boost::python::api::object fromAtoms=0,
boost::python::api::object ignoreAtoms=0)
======================================================================
ERROR: testHashedAtomPairs (__main__.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/chupvl/scisoft/rdkit/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py",
line 66, in testHashedAtomPairs
fp1 = rdMD.GetHashedAtomPairFingerprintAsBitVect(m,2048)
ArgumentError: Python argument types in
rdkit.Chem.rdMolDescriptors.GetHashedAtomPairFingerprintAsBitVect(Mol,
int)
did not match C++ signature:
GetHashedAtomPairFingerprintAsBitVect(RDKit::ROMol, unsigned int,
unsigned int mol, unsigned int nBits=2048, std::vector<unsigned int,
std::allocator<unsigned int> > const* minLength=1, std::vector<unsigned
int, std::allocator<unsigned int> > const* maxLength=30)
======================================================================
ERROR: testMorganFingerprints (__main__.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/chupvl/scisoft/rdkit/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py",
line 132, in testMorganFingerprints
fp = rdMD.GetHashedMorganFingerprint(mol,0)
AttributeError: 'module' object has no attribute
'GetHashedMorganFingerprint'
----------------------------------------------------------------------
Ran 13 tests in 0.007s
FAILED (errors=3)
<end of output>
Test time = 0.10 sec
----------------------------------------------------------
Test Failed.
"pyMolDescriptors" end time: Aug 17 10:38 EDT
"pyMolDescriptors" time elapsed: 00:00:00
----------------------------------------------------------
61/76 Testing: pyGraphMolWrap
61/76 Test: pyGraphMolWrap
Command: "/usr/bin/python"
"/home/chupvl/scisoft/rdkit/Code/GraphMol/Wrap/rough_test.py"
Directory: /home/chupvl/scisoft/rdkit/build/Code/GraphMol/Wrap
"pyGraphMolWrap" start time: Aug 17 10:39 EDT
Output:
----------------------------------------------------------
..............[10:39:03] SMARTS Parse Error: syntax error while parsing:
fiib
28
28
...E.[10:39:03] SMILES Parse Error: syntax error while parsing: fail
[10:39:03] ERROR: Smiles parse error on line 2
[10:39:03] ERROR: Cannot create molecule from : 'fail'
>>> This may result in an infinite loop. It should finish almost instantly
<<< OK, it finished.
............[10:39:03] Explicit valence for atom # 1 C, 5, is greater than
permitted
............FE...................EEEEEEEEE
<end of output>
Test time = 0.32 sec
----------------------------------------------------------
Test Failed.
"pyGraphMolWrap" end time: Aug 17 10:39 EDT
"pyGraphMolWrap" time elapsed: 00:00:00
----------------------------------------------------------
69/76 Testing: pyFeatures
69/76 Test: pyFeatures
Command: "/usr/bin/python"
"/home/chupvl/scisoft/rdkit/Code/ChemicalFeatures/Wrap/testFeatures.py"
Directory: /home/chupvl/scisoft/rdkit/build/Code/ChemicalFeatures/Wrap
"pyFeatures" start time: Aug 17 10:39 EDT
Output:
----------------------------------------------------------
EE
======================================================================
ERROR: testBasic (__main__.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/chupvl/scisoft/rdkit/Code/ChemicalFeatures/Wrap/testFeatures.py",
line 37, in testBasic
ffeat.SetId(123)
AttributeError: 'FreeChemicalFeature' object has no attribute 'SetId'
======================================================================
ERROR: testPickle (__main__.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/chupvl/scisoft/rdkit/Code/ChemicalFeatures/Wrap/testFeatures.py",
line 69, in testPickle
ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor",
"HBondDonor1", geom.Point3D(1.0, 2.0, 3.0),123)
ArgumentError: Python argument types in
FreeChemicalFeature.__init__(FreeChemicalFeature, str, str, Point3D,
int)
did not match C++ signature:
__init__(_object*, std::string family, RDGeom::Point3D loc)
__init__(_object*, std::string family, std::string type,
RDGeom::Point3D loc)
__init__(_object*)
__init__(_object*, std::string)
----------------------------------------------------------------------
Ran 2 tests in 0.000s
FAILED (errors=2)
Testing ChemicalFeatures Wrapper code:
<end of output>
Test time = 0.10 sec
----------------------------------------------------------
Test Failed.
"pyFeatures" end time: Aug 17 10:39 EDT
"pyFeatures" time elapsed: 00:00:00
----------------------------------------------------------
76/76 Testing: pythonTestDirChem
76/76 Test: pythonTestDirChem
Command: "/usr/bin/python"
"/home/chupvl/scisoft/rdkit/rdkit/Chem/test_list.py" "--testDir"
"/home/chupvl/scisoft/rdkit/rdkit/Chem"
Directory: /home/chupvl/scisoft/rdkit/build/rdkit
"pythonTestDirChem" start time: Aug 17 10:39 EDT
Output:
----------------------------------------------------------
....
----------------------------------------------------------------------
Ran 4 tests in 0.050s
OK
......
----------------------------------------------------------------------
Ran 6 tests in 0.050s
OK
....[10:39:30]
****
Pre-condition Violation
valence not defined for atoms not associated with molecules
Violation occurred on line 259 in file
/build/buildd/rdkit-201106+dfsg/Code/GraphMol/Atom.cpp
Failed Expression: dp_mol
****
------------------------------------------------------------------------------
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