On Sat, Jan 26, 2019 at 12:16 AM Xuan Cao <danis....@hotmail.com> wrote:
> > 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. > Yes, that's correct. If "python -c 'import rdkit'" gives you a "No module named rdkit" error, then your PYTHONPATH isn't right. It really sounds like you haven't followed the install instructions exactly. Please take a look at them again, try to follow them exactly, and if that fails then provide here: 1) The name of the directory where the rdkit source is 2) The name of the directory where you did your build 3) *exactly* what commands you executed for "cmake" and "make" 4) The values of $RDBASE, $LD_LIBRARY_PATH, and $PYTHONPATH 5) The exact error text, from the command "python -c 'import rdkit'" Best, -greg > > 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 <greg.land...@gmail.com> > *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 <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:$PYTHONPATH" > > After I reconfigure the path, should I do the cmake .. again? or can I > just run make build, etc.? > > Thank you! > Xuan > ------------------------------ > *From:* Greg Landrum <greg.land...@gmail.com> > *Sent:* January 24, 2019 20:52 > *To:* Xuan Cao > *Cc:* Paolo Tosco; rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] ctest failed while trying to build the > rdkit from source > > Hi, > > Please include the error messages you see when you run one of the tests. > For example, try doing: > ctest -R testData --output-on-failure > and send that output along. > > > > On Thu, Jan 24, 2019 at 10:30 PM Xuan Cao <danis....@hotmail.com> wrote: > > Hi, > > Thank you for the suggestion, but I have already setup the path with > following line before cmake .. > > export RDBASE=/opt/RDKit_20XX_XX_X > export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH > export PYTHONPATH=$RDBASE:$PYTHONPATH > > Xuan > ------------------------------ > *From:* Paolo Tosco <paolo.tosco.m...@gmail.com> > *Sent:* January 24, 2019 14:04 > *To:* rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] ctest failed while trying to build the > rdkit from source > > > Hi Xuan, > > > try to > > > export RDBASE=/absolute/path/to/rdkit > > export PYTHONPATH=$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 <danis....@hotmail.com> <danis....@hotmail.com> > *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 <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 > listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > _______________________________________________ > Rdkit-discuss mailing list > 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 > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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