[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 ", 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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source
Hi, Thank you for the suggestion, but I have already setup the path with following line before cmake .. export RDBASE=/opt/RDKit_20XX_XX_X export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH export PYTHONPATH=$RDBASE:$PYTHONPATH Xuan From: Paolo Tosco Sent: January 24, 2019 14:04 To: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source Hi Xuan, try to export RDBASE=/absolute/path/to/rdkit export PYTHONPATH=$RDBASE export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH then re-run ctest. Cheers, p. On 01/24/19 20:48, Xuan Cao wrote: Sorry, forgot to attach the file From: Xuan Cao <mailto:danis@hotmail.com> Sent: January 24, 2019 13:44 To: rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net> 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 ", 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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source
Sorry, forgot to attach the file From: Xuan Cao Sent: January 24, 2019 13:44 To: rdkit-discuss@lists.sourceforge.net 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 ", 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 a
[Rdkit-discuss] Does RDKit Java have the functionality for calculating the 3D descriptors?
Hi, I am using the RDKit in java. I found that 2D descriptors can be calculated through the RDKFuncs.class, but I couldn't find the 3D descriptors. Thanks for help! Xuan ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source
Hi, Thank you for your help! I think I set the wrong path. For $RDBASE, it should be something like this "/opt/rdkit-Release_2018_09_1" For $LD_LIBRARY_PATH, the documents mentioned that it should include $RDBASE and the boost library, so should it be like this: "export LD_LIBRARY_PATH=$RDBASE:/usr/lib/x86_64-linux-gnu/:$LD_LIBRARY_PATH" (/usr/lib/x86_64-linux-gnu/ is the boost shared library For PYTHONPATH, I did "export PYTHONPATH:$RDBASE:$PYTHONPATH" After I reconfigure the path, should I do the cmake .. again? or can I just run make build, etc.? Thank you! Xuan From: Greg Landrum Sent: January 24, 2019 20:52 To: Xuan Cao Cc: Paolo Tosco; rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source Hi, Please include the error messages you see when you run one of the tests. For example, try doing: ctest -R testData --output-on-failure and send that output along. On Thu, Jan 24, 2019 at 10:30 PM Xuan Cao mailto:danis@hotmail.com>> wrote: Hi, Thank you for the suggestion, but I have already setup the path with following line before cmake .. export RDBASE=/opt/RDKit_20XX_XX_X export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH export PYTHONPATH=$RDBASE:$PYTHONPATH Xuan From: Paolo Tosco mailto:paolo.tosco.m...@gmail.com>> Sent: January 24, 2019 14:04 To: rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net> Subject: Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source Hi Xuan, try to export RDBASE=/absolute/path/to/rdkit export PYTHONPATH=$RDBASE export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH then re-run ctest. Cheers, p. On 01/24/19 20:48, Xuan Cao wrote: Sorry, forgot to attach the file From: Xuan Cao <mailto:danis@hotmail.com> Sent: January 24, 2019 13:44 To: rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net> 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 ", 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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source
Hi, I guess I still couldn't resolve the path issue. After trying to set the path the ctest still fail 70% of test case. The most common error is ImportError: No module named rdkit; I guess I didn't set the python path correctly. Here is my current path on ubuntu $RDBASE bash: /opt/rdkit-Release_2018_09_1: Is a directory $LD_LIBRARY_PATH bash: /opt/rdkit-Release_2018_09_1:/usr/lib/x86_64-linux-gnu::: No such file or directory $PYTHONPATH bash: /opt/rdkit-Release_2018_09_1::: No such file or directory (I also tried: /opt/rdkit-Release_2018_09_1:/usr/local/lib/python3.6/dis-packages: and : /opt/rdkit-Release_2018_09_1:/usr/lib/python3.6: ) Did I do something wrong? Thank you! Xuan From: Greg Landrum Sent: January 25, 2019 9:30 To: Xuan Cao Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source After you change the path you should be able to just run ctest again. On Fri, Jan 25, 2019 at 5:17 PM Xuan Cao mailto:danis@hotmail.com>> wrote: Hi, Thank you for your help! I think I set the wrong path. For $RDBASE, it should be something like this "/opt/rdkit-Release_2018_09_1" For $LD_LIBRARY_PATH, the documents mentioned that it should include $RDBASE and the boost library, so should it be like this: "export LD_LIBRARY_PATH=$RDBASE:/usr/lib/x86_64-linux-gnu/:$LD_LIBRARY_PATH" (/usr/lib/x86_64-linux-gnu/ is the boost shared library For PYTHONPATH, I did "export PYTHONPATH:$RDBASE:$PYTHONPATH" After I reconfigure the path, should I do the cmake .. again? or can I just run make build, etc.? Thank you! Xuan From: Greg Landrum mailto:greg.land...@gmail.com>> Sent: January 24, 2019 20:52 To: Xuan Cao Cc: Paolo Tosco; rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net> Subject: Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source Hi, Please include the error messages you see when you run one of the tests. For example, try doing: ctest -R testData --output-on-failure and send that output along. On Thu, Jan 24, 2019 at 10:30 PM Xuan Cao mailto:danis@hotmail.com>> wrote: Hi, Thank you for the suggestion, but I have already setup the path with following line before cmake .. export RDBASE=/opt/RDKit_20XX_XX_X export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH export PYTHONPATH=$RDBASE:$PYTHONPATH Xuan From: Paolo Tosco mailto:paolo.tosco.m...@gmail.com>> Sent: January 24, 2019 14:04 To: rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net> Subject: Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source Hi Xuan, try to export RDBASE=/absolute/path/to/rdkit export PYTHONPATH=$RDBASE export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH then re-run ctest. Cheers, p. On 01/24/19 20:48, Xuan Cao wrote: Sorry, forgot to attach the file From: Xuan Cao <mailto:danis@hotmail.com> Sent: January 24, 2019 13:44 To: rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net> 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 ", 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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists
