[Rdkit-discuss] C++ building from source, ctest failures under Ubuntu 18.04.4 LTS VM
found anything helpful, but that could also be because I'm unsure for what terms to search. Has anyone seen this before? Does anyone have any suggestions of what I might look at to proceed? Any guidance anyone could offer in this area would be most appreciated. Thank you in advance. Earl Higgins 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. ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit from source under Ubuntu VM, ctest 87 tests failed out of 165. Any advice much appreciated.
Paolo, Thank you for your rapid reply. It's a great suggestion, we are getting somewhere. I ran the first Python test with the "-V" (verbose?) option and, as you can see from the output below, Python is having a problem finding the rdkit module. Do you have any suggestions on how to fix this? Thank you so much. Earl Higgins $ RDBASE=~/conda-rdkit/rdkit ctest -I 2,2 -V UpdateCTestConfiguration from :/home/deep/conda-rdkit/rdkit/build/DartConfiguration.tcl Parse Config file:/home/deep/conda-rdkit/rdkit/build/DartConfiguration.tcl Add coverage exclude regular expressions. SetCTestConfiguration:CMakeCommand:/home/deep/anaconda3/bin/cmake UpdateCTestConfiguration from :/home/deep/conda-rdkit/rdkit/build/DartConfiguration.tcl Parse Config file:/home/deep/conda-rdkit/rdkit/build/DartConfiguration.tcl Test project /home/deep/conda-rdkit/rdkit/build Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 2 Start 2: pyCoordGen 2: Test command: /home/deep/anaconda3/bin/python "/home/deep/conda-rdkit/rdkit/External/CoordGen/Wrap/testCoordGen.py" 2: Test timeout computed to be: 1500 2: Traceback (most recent call last): 2: File "/home/deep/conda-rdkit/rdkit/External/CoordGen/Wrap/testCoordGen.py", line 13, in 2: from rdkit.Chem import rdCoordGen, rdMolAlign 2: ModuleNotFoundError: No module named 'rdkit' 1/1 Test #2: pyCoordGen ...***Failed0.07 sec 0% tests passed, 1 tests failed out of 1 Total Test time (real) = 0.09 sec The following tests FAILED: 2 - pyCoordGen (Failed) Errors while running CTest From: Paolo Tosco Dear Earl, given that all Python tests are failing my guess is that you might be running the tests with a Python interpreter different from the one you have built RDKit against. Re-run one of the failing tests with -V ctest -I 2,2 -V to get some more information. Cheers, p. On 13/03/2020 15:56, Earl Higgins wrote: I am new to RDKit, and my goal is to be able to build it from source ... and I'm surprised at 87/165 test case failures right out of the box ... Any guidance anyone could offer in this area would be most appreciated. Thank you in advance... 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. ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Building RDKit from source under Ubuntu VM, ctest 87 tests failed out of 165. Any advice much appreciated.
CDash.org server in order to be able to view the results, or are they available in some local log file somewhere? Has anyone else experienced this, and if so were you able to correct or fix the test case failures? I have searched through the archives of this discussion list, but not found anything helpful, but that could also be because I'm unsure for what terms to search. Any guidance anyone could offer in this area would be most appreciated. Thank you in advance. Earl Higgins 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. ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss