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:$PYTHONPATH" After I reconfigure the path, should I do the cmake .. again? or can I just run make build, etc.? Thank you! Xuan ________________________________ From: Greg Landrum <greg.land...@gmail.com> Sent: January 24, 2019 20:52 To: Xuan Cao Cc: Paolo Tosco; rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source Hi, Please include the error messages you see when you run one of the tests. For example, try doing: ctest -R testData --output-on-failure and send that output along. On Thu, Jan 24, 2019 at 10:30 PM Xuan Cao <danis....@hotmail.com<mailto:danis....@hotmail.com>> wrote: Hi, Thank you for the suggestion, but I have already setup the path with following line before cmake .. export RDBASE=/opt/RDKit_20XX_XX_X export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH export PYTHONPATH=$RDBASE:$PYTHONPATH Xuan ________________________________ From: Paolo Tosco <paolo.tosco.m...@gmail.com<mailto:paolo.tosco.m...@gmail.com>> Sent: January 24, 2019 14:04 To: rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net> Subject: Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source Hi Xuan, try to export RDBASE=/absolute/path/to/rdkit export PYTHONPATH=$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 <danis....@hotmail.com><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 <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 _______________________________________________ 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
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