Did you start a new bash shell to get those environment variables set? Just
editing that file does not set them.
-David
> On Sep 24, 2014, at 5:22 AM, Shantheya Balasupramaniam
> <[email protected]> wrote:
>
>
> Dear Sir or Madam,
>
> i tried to install the RDKit on ubuntu 14.04 (64bit):
>
> first I installed the pre-requisites by:
>
> sudo apt-get install flex bison build-essential python-numpy cmake python-dev
> sqlite3 libsqlite3-dev libboost-dev libboost-python-dev libboost-regex-dev
>
> afterwards I 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
> mkdir build
> cd build
> cmake ..
> make # -j 4
> make install
>
> 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]
> ------------------------------------------------------------------------------
> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
> _______________________________________________
> Rdkit-discuss mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
------------------------------------------------------------------------------
Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
