Dear Sir or Madam,
i tried to install the RDKit on ubuntu 14.04 (64bit):
first I installed the pre-requisites by:
sudo apt-getinstall flex bison build-essential python-numpy cmake
python-dev sqlite3 libsqlite3-dev libboost-dev libboost-python-dev
libboost-regex-dev
afterwardsI downloaded RDKit_2014_03_1.tgz, unzipped it and copied the
RDKit_2014_03_1 file to /opt
then I edited the bash.bashrc in /etc by:
export RDBASE=/opt/RDKit_2014_03_1
export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$RDBASE:$PYTHONPATH
finally I compiled and installed RDKit by:
cd$RDBASE
mkdirbuild
cdbuild
cmake..
make# -j 4
makeinstall
when I did the ctest as sudo I got this:
Test project /opt/RDKit_2014_03_1/build
Start 1: testDict
1/78 Test #1: testDict ......................... Passed 0.03 sec
Start 2: testDataStructs
2/78 Test #2: testDataStructs ..................***Exception: Other
0.19 sec
Start 3: pyBV
3/78 Test #3: pyBV .............................***Failed 0.01 sec
Start 4: pyDiscreteValueVect
4/78 Test #4: pyDiscreteValueVect ..............***Failed 0.01 sec
Start 5: pySparseIntVect
5/78 Test #5: pySparseIntVect ..................***Failed 0.01 sec
Start 6: testTransforms
6/78 Test #6: testTransforms ................... Passed 0.01 sec
Start 7: testGrid
7/78 Test #7: testGrid .........................***Exception: Other
0.19 sec
Start 8: testPyGeometry
8/78 Test #8: testPyGeometry ...................***Failed 0.01 sec
Start 9: testMatrices
9/78 Test #9: testMatrices ..................... Passed 0.00 sec
Start 10: testAlignment
10/78 Test #10: testAlignment .................... Passed 0.00 sec
Start 11: pyAlignment
11/78 Test #11: pyAlignment ......................***Failed 0.01 sec
Start 12: testOptimizer
12/78 Test #12: testOptimizer .................... Passed 0.00 sec
Start 13: testUFFForceField
13/78 Test #13: testUFFForceField ................ Passed 0.04 sec
Start 14: testMMFFForceField
14/78 Test #14: testMMFFForceField ...............***Exception: Other
0.20 sec
Start 15: pyForceFieldConstraints
15/78 Test #15: pyForceFieldConstraints ..........***Failed 0.01 sec
Start 16: testDistGeom
16/78 Test #16: testDistGeom ..................... Passed 0.00 sec
Start 17: pyDistGeom
17/78 Test #17: pyDistGeom .......................***Failed 0.01 sec
Start 18: graphmolTest1
18/78 Test #18: graphmolTest1 .................... Passed 0.11 sec
Start 19: graphmolcpTest
19/78 Test #19: graphmolcpTest ................... Passed 0.01 sec
Start 20: graphmolqueryTest
20/78 Test #20: graphmolqueryTest ................ Passed 0.01 sec
Start 21: graphmolMolOpsTest
21/78 Test #21: graphmolMolOpsTest ...............***Exception:
SegFault 0.31 sec
Start 22: graphmoltestCanon
22/78 Test #22: graphmoltestCanon ................ Passed 0.00 sec
Start 23: graphmoltestChirality
23/78 Test #23: graphmoltestChirality ............***Exception: Other
0.22 sec
Start 24: graphmoltestPickler
24/78 Test #24: graphmoltestPickler ..............***Exception: Other
0.18 sec
Start 25: graphmolIterTest
25/78 Test #25: graphmolIterTest ................. Passed 0.01 sec
Start 26: testDepictor
26/78 Test #26: testDepictor .....................***Exception: Other
0.18 sec
Start 27: pyDepictor
27/78 Test #27: pyDepictor .......................***Failed 0.01 sec
Start 28: smiTest1
28/78 Test #28: smiTest1 ......................... Passed 0.21 sec
Start 29: smaTest1
29/78 Test #29: smaTest1 ......................... Passed 0.88 sec
Start 30: fileParsersTest1
30/78 Test #30: fileParsersTest1 .................***Exception: Other
0.18 sec
Start 31: testMolSupplier
31/78 Test #31: testMolSupplier ..................***Exception: Other
0.18 sec
Start 32: testMolWriter
32/78 Test #32: testMolWriter ....................***Exception: Other
0.18 sec
Start 33: testTplParser
33/78 Test #33: testTplParser ....................***Exception: Other
0.18 sec
Start 34: testMol2ToMol
34/78 Test #34: testMol2ToMol ....................***Exception: Other
0.19 sec
Start 35: testSubstructMatch
35/78 Test #35: testSubstructMatch ............... Passed 0.01 sec
Start 36: testReaction
36/78 Test #36: testReaction .....................***Exception: Other
0.27 sec
Start 37: pyChemReactions
37/78 Test #37: pyChemReactions ..................***Failed 0.01 sec
Start 38: testChemTransforms
38/78 Test #38: testChemTransforms ...............***Exception: Other
0.26 sec
Start 39: testSubgraphs1
39/78 Test #39: testSubgraphs1 ................... Passed 0.25 sec
Start 40: testSubgraphs2
40/78 Test #40: testSubgraphs2 ................... Passed 0.01 sec
Start 41: testFragCatalog
41/78 Test #41: testFragCatalog ..................***Exception: Other
0.19 sec
Start 42: pyFragCatalog
42/78 Test #42: pyFragCatalog ....................***Failed 0.01 sec
Start 43: testDescriptors
43/78 Test #43: testDescriptors ..................***Exception: Other
0.40 sec
Start 44: pyMolDescriptors
44/78 Test #44: pyMolDescriptors .................***Failed 0.01 sec
Start 45: testFingerprints
45/78 Test #45: testFingerprints .................***Exception: Other
0.31 sec
Start 46: pyPartialCharges
46/78 Test #46: pyPartialCharges .................***Failed 0.01 sec
Start 47: testMolTransforms
47/78 Test #47: testMolTransforms ................***Exception: Other
0.22 sec
Start 48: pyMolTransforms
48/78 Test #48: pyMolTransforms ..................***Failed 0.01 sec
Start 49: testMMFFForceFieldHelpers
49/78 Test #49: testMMFFForceFieldHelpers ........***Exception: Other
0.38 sec
Start 50: testUFFForceFieldHelpers
50/78 Test #50: testUFFForceFieldHelpers .........***Exception: Other
0.27 sec
Start 51: pyForceFieldHelpers
51/78 Test #51: pyForceFieldHelpers ..............***Failed 0.01 sec
Start 52: testDistGeomHelpers
52/78 Test #52: testDistGeomHelpers ..............***Exception: Other
0.11 sec
Start 53: pyDistGeom
53/78 Test #53: pyDistGeom .......................***Failed 0.01 sec
Start 54: testMolAlign
54/78 Test #54: testMolAlign .....................***Exception: Other
0.19 sec
Start 55: pyMolAlign
55/78 Test #55: pyMolAlign .......................***Failed 0.01 sec
Start 56: testFeatures
56/78 Test #56: testFeatures .....................***Exception: Other
0.10 sec
Start 57: pyChemicalFeatures
57/78 Test #57: pyChemicalFeatures ...............***Failed 0.01 sec
Start 58: testShapeHelpers
58/78 Test #58: testShapeHelpers .................***Exception: Other
0.21 sec
Start 59: pyShapeHelpers
59/78 Test #59: pyShapeHelpers ...................***Failed 0.01 sec
Start 60: testMolCatalog
60/78 Test #60: testMolCatalog ................... Passed 0.01 sec
Start 61: pyMolCatalog
61/78 Test #61: pyMolCatalog .....................***Failed 0.01 sec
Start 62: testSLNParse
62/78 Test #62: testSLNParse ..................... Passed 0.02 sec
Start 63: pySLNParse
63/78 Test #63: pySLNParse .......................***Failed 0.01 sec
Start 64: pyGraphMolWrap
64/78 Test #64: pyGraphMolWrap ...................***Failed 0.03 sec
Start 65: pyTestConformerWrap
65/78 Test #65: pyTestConformerWrap ..............***Failed 0.01 sec
Start 66: testQuery
66/78 Test #66: testQuery ........................ Passed 0.00 sec
Start 67: testMatCalc
67/78 Test #67: testMatCalc ...................... Passed 0.00 sec
Start 68: pyMatCalc
68/78 Test #68: pyMatCalc ........................***Failed 0.01 sec
Start 69: pyRanker
69/78 Test #69: pyRanker .........................***Failed 0.01 sec
Start 70: testChemicalFeatures
70/78 Test #70: testChemicalFeatures ............. Passed 0.00 sec
Start 71: pyFeatures
71/78 Test #71: pyFeatures .......................***Failed 0.01 sec
Start 72: pythonTestDbCLI
72/78 Test #72: pythonTestDbCLI ..................***Failed 0.01 sec
Start 73: pythonTestDirML
73/78 Test #73: pythonTestDirML ..................***Failed 0.01 sec
Start 74: pythonTestDirDataStructs
74/78 Test #74: pythonTestDirDataStructs ......... Passed 0.01 sec
Start 75: pythonTestDirDbase
75/78 Test #75: pythonTestDirDbase ............... Passed 0.01 sec
Start 76: pythonTestDirSimDivFilters
76/78 Test #76: pythonTestDirSimDivFilters ....... Passed 0.01 sec
Start 77: pythonTestDirVLib
77/78 Test #77: pythonTestDirVLib ................ Passed 0.01 sec
Start 78: pythonTestDirChem
78/78 Test #78: pythonTestDirChem ................***Failed 0.01 sec
33% tests passed, 52 tests failed out of 78
Total Test time (real) = 7.31 sec
The following tests FAILED:
2 - testDataStructs (OTHER_FAULT)
3 - pyBV (Failed)
4 - pyDiscreteValueVect (Failed)
5 - pySparseIntVect (Failed)
7 - testGrid (OTHER_FAULT)
8 - testPyGeometry (Failed)
11 - pyAlignment (Failed)
14 - testMMFFForceField (OTHER_FAULT)
15 - pyForceFieldConstraints (Failed)
17 - pyDistGeom (Failed)
21 - graphmolMolOpsTest (SEGFAULT)
23 - graphmoltestChirality (OTHER_FAULT)
24 - graphmoltestPickler (OTHER_FAULT)
26 - testDepictor (OTHER_FAULT)
27 - pyDepictor (Failed)
30 - fileParsersTest1 (OTHER_FAULT)
31 - testMolSupplier (OTHER_FAULT)
32 - testMolWriter (OTHER_FAULT)
33 - testTplParser (OTHER_FAULT)
34 - testMol2ToMol (OTHER_FAULT)
36 - testReaction (OTHER_FAULT)
37 - pyChemReactions (Failed)
38 - testChemTransforms (OTHER_FAULT)
41 - testFragCatalog (OTHER_FAULT)
42 - pyFragCatalog (Failed)
43 - testDescriptors (OTHER_FAULT)
44 - pyMolDescriptors (Failed)
45 - testFingerprints (OTHER_FAULT)
46 - pyPartialCharges (Failed)
47 - testMolTransforms (OTHER_FAULT)
48 - pyMolTransforms (Failed)
49 - testMMFFForceFieldHelpers (OTHER_FAULT)
50 - testUFFForceFieldHelpers (OTHER_FAULT)
51 - pyForceFieldHelpers (Failed)
52 - testDistGeomHelpers (OTHER_FAULT)
53 - pyDistGeom (Failed)
54 - testMolAlign (OTHER_FAULT)
55 - pyMolAlign (Failed)
56 - testFeatures (OTHER_FAULT)
57 - pyChemicalFeatures (Failed)
58 - testShapeHelpers (OTHER_FAULT)
59 - pyShapeHelpers (Failed)
61 - pyMolCatalog (Failed)
63 - pySLNParse (Failed)
64 - pyGraphMolWrap (Failed)
65 - pyTestConformerWrap (Failed)
68 - pyMatCalc (Failed)
69 - pyRanker (Failed)
71 - pyFeatures (Failed)
72 - pythonTestDbCLI (Failed)
73 - pythonTestDirML (Failed)
78 - pythonTestDirChem (Failed)
Errors while running CTest
I am not able to find the problem in here.
May you help me?
Best regards,
shantheya
--
Shantheya Balasupramaniam
Technische Universitaet Braunschweig
Institut fuer Medizinische und Pharmazeutische Chemie
Arbeitskreis Prof. Dr. Knut Baumann
Beethovenstrasse 55
D-38106 Braunschweig
Tel.: ++49 531 391-2752
Email: [email protected]
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