Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source
On Sat, Jan 26, 2019 at 12:16 AM Xuan Cao 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 > *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 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:$PYTHONPATH" > > After I reconfigure the path, should I do the cmake .. again? or can I > just run make build, etc.? > > Thank you! > Xuan > -- > *From:* Greg Landrum > *Sent:* January 24, 2019 20:52 > *To:* Xuan Cao > *Cc:* Paolo Tosco; rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] ctest failed while trying to build the > rdkit from source > > Hi, > > Please include the error messages you see when you run one of the tests. > For example, try doing: > ctest -R testData --output-on-failure > and send that output along. > > > > On Thu, Jan 24, 2019 at 10:30 PM Xuan Cao wrote: > > Hi, > > Thank you for the suggestion, but I have already setup the path with > following line before cmake .. > > export RDBASE=/opt/RDKit_20XX_XX_X > export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH > export PYTHONPATH=$RDBASE:$PYTHONPATH > > Xuan > -- > *From:* Paolo Tosco > *Sent:* January 24, 2019 14:04 > *To:* rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] ctest failed while trying to build the > rdkit from source > > > Hi Xuan, > > > try to > > > export RDBASE=/absolute/path/to/rdkit > > export PYTHONPATH=$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 > *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. > &g
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>
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 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:$PYTHONPATH" > > After I reconfigure the path, should I do the cmake .. again? or can I > just run make build, etc.? > > Thank you! > Xuan > -- > *From:* Greg Landrum > *Sent:* January 24, 2019 20:52 > *To:* Xuan Cao > *Cc:* Paolo Tosco; rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] ctest failed while trying to build the > rdkit from source > > Hi, > > Please include the error messages you see when you run one of the tests. > For example, try doing: > ctest -R testData --output-on-failure > and send that output along. > > > > On Thu, Jan 24, 2019 at 10:30 PM Xuan Cao wrote: > > Hi, > > Thank you for the suggestion, but I have already setup the path with > following line before cmake .. > > export RDBASE=/opt/RDKit_20XX_XX_X > export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH > export PYTHONPATH=$RDBASE:$PYTHONPATH > > Xuan > -- > *From:* Paolo Tosco > *Sent:* January 24, 2019 14:04 > *To:* rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] ctest failed while trying to build the > rdkit from source > > > Hi Xuan, > > > try to > > > export RDBASE=/absolute/path/to/rdkit > > export PYTHONPATH=$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 > *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 > > > > > > > > ___ > 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
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, 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 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 > *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:$LD_LIBRARY_PATH > > > then re-run ctest. > > > Cheers, > > p. > > On 01/24/19 20:48, Xuan Cao wrote: > > Sorry, forgot to attach the file > > ---------- > *From:* Xuan Cao > *Sent:* January 24, 2019 13:44 > *To:* rdkit-discuss@lists.sourceforge.net > *Subject:* [Rdkit-discuss] ctest failed while trying to build the rdkit > from source > > Hi, > > I am trying to build the rdkit from source on a fresh new ubuntu18.04 > virutal machine with virtual box (I did sudo apt update; sudo apt upgrade; > etc.). > > I successfully executed "sudo cmake ..", "sudo make", "sudo make install" > commands, but the sudo ctest gave me only 29% tests passed (I attached file > with failed test). > > Then I tried the c++ example from rdkit/Docs/Book/. When I compile the > code with "#include ", the system couldn't find the > the header file: GraphMol/GraphMol.h. > > I also tried to directly import rdkit by executing "from rdkit import > Chem" from python script, but it complain about no module named "rdkit". > > I know that conda install works (I can import rdkit with conda), but I > want to use rdkit functionalities without any virtual environment, so I > choose to build from source. > > Is there any suggestion that can help to use rdkit from source without any > virtualenv (python or cpp)? > > Any help appreciated! > > Thanks! > Xuan > > > > > > > > ___ > Rdkit-discuss mailing > listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ctest failed while trying to build the rdkit from source
Hi, Thank you for the suggestion, but I have already setup the path with following line before cmake .. export RDBASE=/opt/RDKit_20XX_XX_X export LD_LIBRARY_PATH=$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
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 *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 ___ 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
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 (Ch
[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
Hi Jim, ctest is a part of the cmake system that is used to build the rdkit: https://cmake.org/ there's great documentation available there. We use ctest after every build to run the RDKit test suite. The idea is to ensure that the code is working as expected. The tests are all run automatically as part of the RDKit-Jenkins integration and the process by which we produce conda builds. In order to run ctest yourself on the RDKit, you have to have a build environment set up (i.e. with an install of Visual Studio) and do an RDKit build. Getting this all setup is "non-trivial", so unless you really want to do RDKit development it's likely not worth doing. If you can provide a bit more info about what you want to do/learn, we may be able to provide some other suggestions. Best, -greg On Sun, Nov 5, 2017 at 8:43 PM, James T. Metz via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > RDkit Experts, > > What is ctest? Is it fully documented somewhere? > > I am running PYTHON 3.5.2/RDkit 2017.03.1 on WINDOWS 7 via > Pycharm 2017.2.3 > > Is it possible to run ctest in this environment? ctest seems to be a > good way > to exercise and test many of the capabilities of RDkit, some of which I am > not familiar with. Thank you. > > Regards, > Jim Metz > > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] ctest
RDkit Experts, What is ctest? Is it fully documented somewhere? I am running PYTHON 3.5.2/RDkit 2017.03.1 on WINDOWS 7 via Pycharm 2017.2.3 Is it possible to run ctest in this environment? ctest seems to be a good way to exercise and test many of the capabilities of RDkit, some of which I am not familiar with. Thank you. Regards, Jim Metz -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ctest fails
Dear Paolo,
Thank you for your response.
I built boost with the following commands.
$ ./bootstrap.sh --prefix=/usr/local/boost_1_62_0
--with-python=/usr/local/bin/python --with-python-root=/usr/local
$ ./b2 threading=multi
/usr/local/bin/python is my self-built version of Python 2.7.
The command you suggested gives the following information but I can not
interpret it.
$ ctest -I 7,7 -V
UpdateCTestConfiguration from :/home/nmr/RDKit/build/DartConfiguration.tcl
Start processing tests
UpdateCTestConfiguration from :/home/nmr/RDKit/build/DartConfiguration.tcl
Test project /home/nmr/RDKit/build
Constructing a list of tests
Done constructing a list of tests
Changing directory into /home/nmr/RDKit/build/External/INCHI-API
Changing directory into /home/nmr/RDKit/build/Code/RDGeneral
Changing directory into /home/nmr/RDKit/build/Code/DataStructs
Changing directory into /home/nmr/RDKit/build/Code/DataStructs/Wrap
7/112 Testing pyBV
Test command: /usr/local/bin/python
/home/nmr/RDKit/Code/DataStructs/Wrap/testBV.py
Test timeout computed to be: 9.99988e+06
..E...E..
==
ERROR: test3Bounds (__main__.TestCase)
--
Traceback (most recent call last):
File "/home/nmr/RDKit/Code/DataStructs/Wrap/testBV.py", line 91, in
test3Bounds
bv1[11]
RuntimeError: IndexErrorException
==
ERROR: test7FPS (__main__.TestCase)
--
Traceback (most recent call last):
File "/home/nmr/RDKit/Code/DataStructs/Wrap/testBV.py", line 172, in test7FPS
self.assertRaises(ValueError, lambda:
DataStructs.CreateFromFPSText("030082801"))
File "/usr/local/lib/python2.7/unittest/case.py", line 475, in assertRaises
callableObj(*args, **kwargs)
File "/home/nmr/RDKit/Code/DataStructs/Wrap/testBV.py", line 172, in
self.assertRaises(ValueError, lambda:
DataStructs.CreateFromFPSText("030082801"))
RuntimeError: ValueErrorException
--
Ran 13 tests in 0.753s
FAILED (errors=2)
-- Process completed
***Failed
Changing directory into /home/nmr/RDKit/build/Code/Geometry
Changing directory into /home/nmr/RDKit/build/Code/Geometry/Wrap
Changing directory into /home/nmr/RDKit/build/Code/Numerics
Changing directory into /home/nmr/RDKit/build/Code/Numerics/Alignment
Changing directory into /home/nmr/RDKit/build/Code/Numerics/Alignment/Wrap
Changing directory into /home/nmr/RDKit/build/Code/Numerics/Optimizer
Changing directory into /home/nmr/RDKit/build/Code/ForceField/UFF
Changing directory into /home/nmr/RDKit/build/Code/ForceField/MMFF
Changing directory into /home/nmr/RDKit/build/Code/ForceField/Wrap
Changing directory into /home/nmr/RDKit/build/Code/DistGeom
Changing directory into /home/nmr/RDKit/build/Code/DistGeom/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Depictor
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Depictor/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/SmilesParse
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/FileParsers
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Substruct
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/ChemReactions
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/ChemReactions/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/ChemTransforms
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Subgraphs
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/FilterCatalog
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/FilterCatalog/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/FragCatalog
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/FragCatalog/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Descriptors
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Descriptors/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/Fingerprints
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/PartialCharges
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/PartialCharges/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/MolTransforms
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/MolTransforms/Wrap
Changing directory into
/home/nmr/RDKit/build/Code/GraphMol/ForceFieldHelpers/MMFF
Changing directory into
/home/nmr/RDKit/build/Code/GraphMol/ForceFieldHelpers/UFF
Changing directory into
/home/nmr/RDKit/build/Code/GraphMol/ForceFieldHelpers/CrystalFF
Changing directory into
/home/nmr/RDKit/build/Code/GraphMol/ForceFieldHelpers/Wrap
Changing directory into /home/nmr/RDKit/build/Code/GraphMol/DistGeomHelpers
Changing directory into /home/nmr/RDKit/build
Re: [Rdkit-discuss] ctest fails
Dear Rintarou, did you check that you built boost 1.62 against your own self-built version of Python 2.7 rather than against system Python? Alternatively, you might be missing a Python module. You may get more information about why, e.g., test 7 failed issuing the command: ctest -I 7,7 -V Best, Paolo On 02/01/17 09:00, 鈴木 倫太郎 wrote: > Dear All, > > I have been used RDKit 2015_03_1 with self-build version of python 2.7 and > boost 1.62 on CentOS 5.11. > Now I tried to built and install 2016_09_3 in the same environment and I got > 13 errors after ctest. > > > 88% tests passed, 13 tests failed out of 112 > > The following tests FAILED: >7 - pyBV (Failed) >8 - pyDiscreteValueVect (Failed) >9 - pySparseIntVect (Failed) > 13 - testPyGeometry (Failed) > 64 - pyMolTransforms (Failed) > 70 - pyDistGeom (Failed) > 72 - pyMolAlign (Failed) > 74 - pyChemicalFeatures (Failed) > 95 - pyGraphMolWrap (Failed) > 97 - pyTestTrajectory (Failed) > 102 - pySimDivPickers (Failed) > 108 - pythonTestDirDataStructs (Failed) > 112 - pythonTestDirChem (Failed) > Errors while running CTest > > > I checked following commands. I could not find problems. > > > $ ldd $RDBASE/rdkit/Chem/rdchem.so > linux-vdso.so.1 => (0x7fff5e3fd000) > libSmilesParse.so.1 => /home/nmr/RDKit/lib/libSmilesParse.so.1 > (0x2b7ccfaa) > libChemTransforms.so.1 => /home/nmr/RDKit/lib/libChemTransforms.so.1 > (0x2b7ccfcf6000) > libSubstructMatch.so.1 => /home/nmr/RDKit/lib/libSubstructMatch.so.1 > (0x2b7ccff39000) > libGraphMol.so.1 => /home/nmr/RDKit/lib/libGraphMol.so.1 > (0x2b7cd0167000) > libRDGeometryLib.so.1 => /home/nmr/RDKit/lib/libRDGeometryLib.so.1 > (0x2b7cd04c9000) > libRDGeneral.so.1 => /home/nmr/RDKit/lib/libRDGeneral.so.1 > (0x2b7cd06e4000) > libRDBoost.so.1 => /home/nmr/RDKit/lib/libRDBoost.so.1 > (0x2b7cd08ff000) > libboost_python.so.1.62.0 => > /usr/local/boost_1_62_0/lib/libboost_python.so.1.62.0 (0x2b7cd0ccb000) > libboost_thread.so.1.62.0 => > /usr/local/boost_1_62_0/lib/libboost_thread.so.1.62.0 (0x2b7cd0f1f000) > libboost_system.so.1.62.0 => > /usr/local/boost_1_62_0/lib/libboost_system.so.1.62.0 (0x2b7cd1145000) > libboost_serialization.so.1.62.0 => > /usr/local/boost_1_62_0/lib/libboost_serialization.so.1.62.0 > (0x2b7cd1349000) > libDataStructs.so.1 => /home/nmr/RDKit/lib/libDataStructs.so.1 > (0x2b7cd1599000) > libpthread.so.0 => /lib64/libpthread.so.0 (0x2b7cd18fd000) > libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x2b7cd1b1a000) > libm.so.6 => /lib64/libm.so.6 (0x2b7cd1e1a000) > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x2b7cd209d000) > libc.so.6 => /lib64/libc.so.6 (0x2b7cd22ac000) > libdl.so.2 => /lib64/libdl.so.2 (0x2b7cd2605000) > libutil.so.1 => /lib64/libutil.so.1 (0x2b7cd280a000) > librt.so.1 => /lib64/librt.so.1 (0x2b7cd2a0d000) > /lib64/ld-linux-x86-64.so.2 (0x003ada20) > > > $ python -c 'from rdkit import rdBase; print rdBase.__file__' > /home/nmr/RDKit/rdkit/rdBase.so > > > Can you please suggest any solutions? > > Thank you, > Rintarou > > > Suzuki, Rintarou > National Agriculture and Food Research Organization > Tsukuba, Japan > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] ctest fails
Dear All, I have been used RDKit 2015_03_1 with self-build version of python 2.7 and boost 1.62 on CentOS 5.11. Now I tried to built and install 2016_09_3 in the same environment and I got 13 errors after ctest. 88% tests passed, 13 tests failed out of 112 The following tests FAILED: 7 - pyBV (Failed) 8 - pyDiscreteValueVect (Failed) 9 - pySparseIntVect (Failed) 13 - testPyGeometry (Failed) 64 - pyMolTransforms (Failed) 70 - pyDistGeom (Failed) 72 - pyMolAlign (Failed) 74 - pyChemicalFeatures (Failed) 95 - pyGraphMolWrap (Failed) 97 - pyTestTrajectory (Failed) 102 - pySimDivPickers (Failed) 108 - pythonTestDirDataStructs (Failed) 112 - pythonTestDirChem (Failed) Errors while running CTest I checked following commands. I could not find problems. $ ldd $RDBASE/rdkit/Chem/rdchem.so linux-vdso.so.1 => (0x7fff5e3fd000) libSmilesParse.so.1 => /home/nmr/RDKit/lib/libSmilesParse.so.1 (0x2b7ccfaa) libChemTransforms.so.1 => /home/nmr/RDKit/lib/libChemTransforms.so.1 (0x2b7ccfcf6000) libSubstructMatch.so.1 => /home/nmr/RDKit/lib/libSubstructMatch.so.1 (0x2b7ccff39000) libGraphMol.so.1 => /home/nmr/RDKit/lib/libGraphMol.so.1 (0x2b7cd0167000) libRDGeometryLib.so.1 => /home/nmr/RDKit/lib/libRDGeometryLib.so.1 (0x2b7cd04c9000) libRDGeneral.so.1 => /home/nmr/RDKit/lib/libRDGeneral.so.1 (0x2b7cd06e4000) libRDBoost.so.1 => /home/nmr/RDKit/lib/libRDBoost.so.1 (0x2b7cd08ff000) libboost_python.so.1.62.0 => /usr/local/boost_1_62_0/lib/libboost_python.so.1.62.0 (0x2b7cd0ccb000) libboost_thread.so.1.62.0 => /usr/local/boost_1_62_0/lib/libboost_thread.so.1.62.0 (0x2b7cd0f1f000) libboost_system.so.1.62.0 => /usr/local/boost_1_62_0/lib/libboost_system.so.1.62.0 (0x2b7cd1145000) libboost_serialization.so.1.62.0 => /usr/local/boost_1_62_0/lib/libboost_serialization.so.1.62.0 (0x2b7cd1349000) libDataStructs.so.1 => /home/nmr/RDKit/lib/libDataStructs.so.1 (0x2b7cd1599000) libpthread.so.0 => /lib64/libpthread.so.0 (0x2b7cd18fd000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x2b7cd1b1a000) libm.so.6 => /lib64/libm.so.6 (0x2b7cd1e1a000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x2b7cd209d000) libc.so.6 => /lib64/libc.so.6 (0x2b7cd22ac000) libdl.so.2 => /lib64/libdl.so.2 (0x2b7cd2605000) libutil.so.1 => /lib64/libutil.so.1 (0x2b7cd280a000) librt.so.1 => /lib64/librt.so.1 (0x2b7cd2a0d000) /lib64/ld-linux-x86-64.so.2 (0x003ada20) $ python -c 'from rdkit import rdBase; print rdBase.__file__' /home/nmr/RDKit/rdkit/rdBase.so Can you please suggest any solutions? Thank you, Rintarou Suzuki, Rintarou National Agriculture and Food Research Organization Tsukuba, Japan -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ctest of new build - testGrid
Dear RDKitters, I just wanted to mention that this issue was resolved - RDBASE was not correctly set. A classical one, at least from mailing listing point of view... Thanks2Greg, Cheers, Paul > > > > when running ctest on a new build, I run into an issue when it comes to > > testGrid - this step takes ages and does not stop... > > Interesting. Can you please send a few pieces of additional information: > 1) the version of the RDKit you're using > 2) The operating system you're working under > 3) the output of the command "ldd Code/Geometry/testGrid", when run > from the build directory > > Thanks, > -greg This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ctest of new build - testGrid
Hi Paul, On Tue, Apr 24, 2012 at 5:54 PM, wrote: > > > when running ctest on a new build, I run into an issue when it comes to > testGrid - this step takes ages and does not stop... Interesting. Can you please send a few pieces of additional information: 1) the version of the RDKit you're using 2) The operating system you're working under 3) the output of the command "ldd Code/Geometry/testGrid", when run from the build directory Thanks, -greg -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] ctest of new build - testGrid
Dear RDKitters, when running ctest on a new build, I run into an issue when it comes to testGrid - this step takes ages and does not stop... Of course, I checked the mail archive and found out some related problems: * --output-on-failure does not give any additional information Simply executing testGrid from Code/Geometry gives: *** Testing Grid - testUniformGrid1 - testUniformGrid2 - testUniformGridPickling Some other tests (prior to the testGrid part) do fail, which should be related to an LD_LIBRARY_PATH / PYTHONPATH setting, according to: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01332.html & http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg02269.html But I guess that it makes sense to first solve the testGrid issue, or are the topics related to each other? Cheers & Thanks, Paul This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
