Re: [Rdkit-discuss] install error
Open-Source Cheminformatics and Machine Learning
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From: Yingfeng W. <ywa...@gm...> - 2013-06-05 15:45:44
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Jan, Thanks. I just found the problem. The environment setting is in .bashrc, which is not for sudo. Now, I install everything in a local directory, and don't need sudo. Then it works now. Sorry about my confusing mistake. Yingfeng On Wed, Jun 5, 2013 at 11:22 AM, Jan Holst Jensen <ja...@bi...>wrote: > OK, that looks fine. And I assume you build directly in > /opt/RDKit_latest/latest/, so 'make install' puts files in > /opt/RDKit_latest/latest/lib/. > > The only other thing that comes to my mind is if your boost libraries are > included in LD_LIBRARY_PATH. > > Cheers > -- Jan > > > On 2013-06-05 16:55, Yingfeng Wang wrote: > > Yes, I did. > > export RDBASE=/opt/RDKit_latest/latest > export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH > export PYTHONPATH=$RDBASE:$PYTHONPATH > > I put them on ~/.bashrc > > > On Wed, Jun 5, 2013 at 10:53 AM, Jan Holst Jensen <ja...@bi...>wrote: > >> Hi Yingfeng, >> >> Looks like what happened to me, when I had forgotten to set the >> environment. Did you set LD_LIBRARY_PATH to $RDBASE/lib before running the >> tests ? >> >> Kind regards >> -- Jan Holst Jensen >> >> >> On 2013-06-05 16:09, Yingfeng Wang wrote: >> >> Yes. I tried again. This time, >> >> after run download-inchi.sh >> >> I >> mkdir build >> cd build >> sudo cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON >> sudo make >> sudo make install >> >> by far, no error reported. >> >> but, when I run sudo ctest >> >> I got >> >> The following tests FAILED: >> 1 - testInchi (OTHER_FAULT) >> 3 - testDataStructs (OTHER_FAULT) >> 4 - pyBV (Failed) >> 5 - pyDiscreteValueVect (Failed) >> 6 - pySparseIntVect (Failed) >> 8 - testGrid (OTHER_FAULT) >> 9 - testPyGeometry (Failed) >> 12 - pyAlignment (Failed) >> 16 - pyDistGeom (Failed) >> 20 - graphmolMolOpsTest (SEGFAULT) >> 22 - graphmoltestChirality (OTHER_FAULT) >> 23 - graphmoltestPickler (OTHER_FAULT) >> 25 - testDepictor (OTHER_FAULT) >> 26 - pyDepictor (Failed) >> 29 - fileParsersTest1 (OTHER_FAULT) >> 30 - testMolSupplier (OTHER_FAULT) >> 31 - testMolWriter (OTHER_FAULT) >> 32 - testTplParser (OTHER_FAULT) >> 33 - testMol2ToMol (OTHER_FAULT) >> 35 - testReaction (OTHER_FAULT) >> 36 - pyChemReactions (Failed) >> 37 - testChemTransforms (OTHER_FAULT) >> 40 - testFragCatalog (OTHER_FAULT) >> 41 - pyFragCatalog (Failed) >> 42 - testDescriptors (OTHER_FAULT) >> 43 - pyMolDescriptors (Failed) >> 44 - testFingerprints (OTHER_FAULT) >> 45 - pyPartialCharges (Failed) >> 46 - testMolTransforms (OTHER_FAULT) >> 47 - pyMolTransforms (Failed) >> 48 - testForceFieldHelpers (OTHER_FAULT) >> 49 - pyForceFieldHelpers (Failed) >> 50 - testDistGeomHelpers (OTHER_FAULT) >> 51 - pyDistGeom (Failed) >> 52 - testMolAlign (OTHER_FAULT) >> 53 - pyMolAlign (Failed) >> 54 - testFeatures (OTHER_FAULT) >> 55 - pyChemicalFeatures (Failed) >> 56 - testShapeHelpers (OTHER_FAULT) >> 57 - pyShapeHelpers (Failed) >> 59 - pyMolCatalog (Failed) >> 61 - pySLNParse (Failed) >> 62 - pyGraphMolWrap (Failed) >> 63 - pyTestConformerWrap (Failed) >> 66 - pyMatCalc (Failed) >> 67 - pyCMIM (Failed) >> 68 - pyRanker (Failed) >> 70 - pyFeatures (Failed) >> 71 - pythonTestDbCLI (Failed) >> 72 - pythonTestDirML (Failed) >> 77 - pythonTestDirChem (Failed) >> Errors while running CTest >> >> Thanks. >> >> >> >> On Wed, Jun 5, 2013 at 5:54 AM, JP <jea...@in...> wrote: >> >>> mmmm, >>> >>> Before running cmake - have you >>> run ./External/INCHI-API/download-inchi.sh ? >>> >>> >>> >>> >>> On 5 June 2013 04:13, Yingfeng Wang <ywa...@gm...> wrote: >>> >>>> After getting the latest code by git, I install RDKit on my ubuntu >>>> 12.04. >>>> >>>> In the step of make install, I got >>>> >>>> CMake Error at External/INCHI-API/cmake_install.cmake:124 (FILE): >>>> >>>> It seems the file $RDBASE/lib/libRDInchiLib.so.1.2013.06.1pre can't >>>> be found. Please note that I have turned on the flag of inchi. >>>> >>>> Thanks. >>>> >>>> Yingfeng >>>> >>>> >> > > |