Sorry, forgot to attach the file
________________________________
From: Xuan Cao <[email protected]>
Sent: January 24, 2019 13:44
To: [email protected]
Subject: [Rdkit-discuss] ctest failed while trying to build the rdkit from
source
Hi,
I am trying to build the rdkit from source on a fresh new ubuntu18.04 virutal
machine with virtual box (I did sudo apt update; sudo apt upgrade; etc.).
I successfully executed "sudo cmake ..", "sudo make", "sudo make install"
commands, but the sudo ctest gave me only 29% tests passed (I attached file
with failed test).
Then I tried the c++ example from rdkit/Docs/Book/. When I compile the code
with "#include <GraphMol/GraphMol.h>", the system couldn't find the the header
file: GraphMol/GraphMol.h.
I also tried to directly import rdkit by executing "from rdkit import Chem"
from python script, but it complain about no module named "rdkit".
I know that conda install works (I can import rdkit with conda), but I want to
use rdkit functionalities without any virtual environment, so I choose to build
from source.
Is there any suggestion that can help to use rdkit from source without any
virtualenv (python or cpp)?
Any help appreciated!
Thanks!
Xuan
The following tests FAILED:
2 - pyCoordGen (Failed)
4 - testRDValue (Child aborted)
5 - testDataStructs (Child aborted)
6 - testFPB (Child aborted)
7 - testMultiFPB (Child aborted)
8 - pyBV (Failed)
9 - pyDiscreteValueVect (Failed)
10 - pySparseIntVect (Failed)
11 - pyFPB (Failed)
13 - testGrid (Child aborted)
14 - testPyGeometry (Failed)
17 - pyAlignment (Failed)
20 - testMMFFForceField (Child aborted)
21 - pyForceFieldConstraints (Failed)
23 - pyDistGeom (Failed)
24 - graphmolTest1 (Child aborted)
27 - graphmolMolOpsTest (SEGFAULT)
29 - graphmoltestChirality (Child aborted)
30 - graphmoltestPickler (Child aborted)
33 - hanoiTest (Child aborted)
35 - resMolSupplierTest (Child aborted)
38 - graphmolTestsCatch (Failed)
39 - testDepictor (Child aborted)
40 - pyDepictor (Failed)
46 - fileParsersTest1 (Child aborted)
47 - testMolSupplier (Child aborted)
48 - testMolWriter (Child aborted)
49 - testTplParser (Child aborted)
50 - testMol2ToMol (Child aborted)
52 - testExtendedStereoParsing (Child aborted)
53 - fileParsersCatchTest (Failed)
54 - testSubstructMatch (Child aborted)
55 - testReaction (Child aborted)
59 - pyChemReactions (Failed)
60 - pyChemReactionEnumerations (Failed)
61 - pyChemReactionSanitize (Failed)
62 - testChemTransforms (Child aborted)
65 - filterCatalogTest (Child aborted)
66 - pyFilterCatalog (Failed)
67 - testFragCatalog (Child aborted)
68 - pyFragCatalog (Failed)
69 - testDescriptors (Child aborted)
70 - testAUTOCORR2D (Child aborted)
71 - pyMolDescriptors (Failed)
72 - pyMolDescriptors3D (Failed)
73 - testFingerprints (Child aborted)
74 - testFingerprintGenerators (Child aborted)
75 - pyTestGenerator (Failed)
77 - pyPartialCharges (Failed)
78 - testMolTransforms (Child aborted)
79 - pyMolTransforms (Failed)
80 - testMMFFForceFieldHelpers (Child aborted)
81 - testUFFForceFieldHelpers (Child aborted)
83 - pyForceFieldHelpers (Failed)
84 - testDistGeomHelpers (Child aborted)
85 - pyDistGeomHelpers (Failed)
86 - testMolAlign (Child aborted)
87 - pyMolAlign (Failed)
88 - testFeatures (Child aborted)
89 - pyChemicalFeatures (Failed)
90 - testShapeHelpers (Child aborted)
91 - pyShapeHelpers (Failed)
93 - pyMolCatalog (Failed)
94 - moldraw2DTest1 (Child aborted)
96 - pyMolDraw2D (Failed)
98 - pyFMCS (Failed)
101 - pyMolHash (Failed)
103 - pyMMPA (Failed)
104 - testStructChecker (Child aborted)
105 - pyStructChecker (Failed)
107 - pyReducedGraphs (Failed)
108 - trajectoryTest (Child aborted)
109 - substructLibraryTest (Child aborted)
110 - pySubstructLibrary (Failed)
112 - pyRGroupDecomposition (Failed)
113 - molInterchangeTest1 (Child aborted)
114 - pyMolInterchange (Failed)
116 - pySLNParse (Failed)
117 - pyGraphMolWrap (Failed)
118 - pyTestConformerWrap (Failed)
119 - pyTestTrajectory (Failed)
120 - pyTestThreads (Failed)
121 - molStandardizeTest (Child aborted)
122 - molNormalizeTest (Child aborted)
123 - molValidateTest (Child aborted)
124 - molChargeTest (Child aborted)
125 - molTautomerTest (Child aborted)
126 - molStandardizeSmallTest (Child aborted)
127 - molFragmentTest (Child aborted)
128 - pyMolStandardize (Failed)
131 - pyMatCalc (Failed)
133 - pySimDivPickers (Failed)
134 - pyRanker (Failed)
136 - pyFeatures (Failed)
137 - pythonTestDbCLI (Failed)
138 - pythonTestDirML (Failed)
139 - pythonTestDirDataStructs (Failed)
140 - pythonTestDirDbase (Failed)
141 - pythonTestDirSimDivFilters (Failed)
142 - pythonTestDirVLib (Failed)
143 - pythonTestDirChem (Failed)
144 - pythonTestSping (Failed)_______________________________________________
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