I have added this into the .bashrc
export RDBASE=/home/chupvl/scisoft/rdkit/
export PYTHONPATH=/home/chupvl/scisoft/rdkit/:/usr/include/python2.7/
export LD_LIBRARY_PATH=/home/chupvl/scisoft/rdkit/lib/
but actually received even *more* Failed messages.
Best regards,
--
Vladimir Chupakhin,
Boston, MA, USA
tel: +1-617-943-9710
LinkedIN: http://www.linkedin.com/in/chupvl
On Fri, Aug 17, 2012 at 11:07 AM, Abhik Seal <abhik1...@gmail.com> wrote:
> Dear Vladimir,
>
> Check the python path . RDBASE must have the python path.
>
>
> Abhik Seal
> Indiana University Bloomington
> Department of Chemical Informatics
> abs...@indiana.edu
> *OSDD CHEMINFORMATICS*
> +18123699097
> http://mypage.iu.edu/~abseal/index.htm
>
>
>
> On Fri, Aug 17, 2012 at 8:29 PM, Vladimir Chupakhin <chu...@gmail.com>wrote:
>
>> 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
>> ****
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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