[Rdkit-discuss] C++ building from source, ctest failures under Ubuntu 18.04.4 LTS VM
Hello, I'm continuing to try to get through the 165 build tests in RDKit. I am
doing a local source build under Ubuntu 18.04.4 LTS running in a VM using
Oracle VirtualBox (host Windows 10). With help from Paolo Tosco (thank you so
much), I was able to get from 87 tests failing down to 47 tests failing. It
turns out it was a environment variable issue with the python tests. Now I am
trying to figure out why the C++ tests are failing.
Focusing in on the first C++ test that fails, which is number 40
(graphmolTestsCatch), I get the following:
$ LD_LIBRARY_PATH=~/conda-rdkit/rdkit/lib PYTHONPATH=~/conda-rdkit/rdkit
RDBASE=~/conda-rdkit/rdkit ctest -I 40,40 -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 40
Start 40: graphmolTestsCatch
40: Test command:
/home/deep/conda-rdkit/rdkit/build/Code/GraphMol/graphmolTestsCatch
40: Test timeout computed to be: 1500
40:
40: ~~~
40: graphmolTestsCatch is a Catch v2.1.2 host application.
40: Run with -? for options
40:
40: ---
40: handling of bondStereoCare in updateQueryProperties
40: fully specified
40: ---
40: /home/deep/conda-rdkit/rdkit/Code/GraphMol/catch_graphmol.cpp:1122
40: ...
40:
40: /home/deep/conda-rdkit/rdkit/Code/GraphMol/catch_graphmol.cpp:1122: FAILED:
40: {Unknown expression after the reported line}
40: due to unexpected exception with message:
40: RingInfo not initialized
40:
40: ---
40: handling of bondStereoCare in updateQueryProperties
40: fully unspecified
40: ---
40: /home/deep/conda-rdkit/rdkit/Code/GraphMol/catch_graphmol.cpp:1153
40: ...
40:
40: /home/deep/conda-rdkit/rdkit/Code/GraphMol/catch_graphmol.cpp:1153: FAILED:
40: {Unknown expression after the reported line}
40: due to unexpected exception with message:
40: RingInfo not initialized
40:
40: ---
40: handling of bondStereoCare in updateQueryProperties
40: partially unspecified
40: ---
40: /home/deep/conda-rdkit/rdkit/Code/GraphMol/catch_graphmol.cpp:1184
40: ...
40:
40: /home/deep/conda-rdkit/rdkit/Code/GraphMol/catch_graphmol.cpp:1184: FAILED:
40: {Unknown expression after the reported line}
40: due to unexpected exception with message:
40: RingInfo not initialized
40:
40: ---
40: handling of bondStereoCare in updateQueryProperties
40: V2000
40: ---
40: /home/deep/conda-rdkit/rdkit/Code/GraphMol/catch_graphmol.cpp:1303
40: ...
40:
40: /home/deep/conda-rdkit/rdkit/Code/GraphMol/catch_graphmol.cpp:1303: FAILED:
40: {Unknown expression after the reported line}
40: due to unexpected exception with message:
40: RingInfo not initialized
40:
40: ---
40: handling of bondStereoCare in updateQueryProperties
40: molecule from SMILES
40: ---
40: /home/deep/conda-rdkit/rdkit/Code/GraphMol/catch_graphmol.cpp:1332
40: ...
40:
40: /home/deep/conda-rdkit/rdkit/Code/GraphMol/catch_graphmol.cpp:1332: FAILED:
40: {Unknown expression after the reported line}
40: due to unexpected exception with message:
40: RingInfo not initialized
40:
40:
===
40: test cases: 27 | 26 passed | 1 failed
40: assertions: 305 | 300 passed | 5 failed
40:
1/1 Test #40: graphmolTestsCatch ...***Failed0.09 sec
0% tests passed, 1 tests failed out of 1
Total Test time (real) = 0.11 sec
The following tests FAILED:
40 - graphmolTestsCatch (Failed)
Errors while running CTest
$
I have searched through the archives of this discussion list, but not found
anythin
Re: [Rdkit-discuss] Looking for additional GSoC co-mentors
Le 01/04/2020 à 08:16, Greg Landrum a écrit : There's more information on the program, including the dates, here: https://summerofcode.withgoogle.com/how-it-works/ GSoC is really a great program and being a mentor/co-mentor is a good way to help move both the open-source community and the RDKit forward. If you're interested or have questions, feel free to send me email, Dear Greg, I'm not sure if I'm the best specifically concerning rdkit internals, but as a teacher, I think I can help. I think I could be more useful on these topics (pick one): - generalized file reader - molecular interaction fields - openMM HTH, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, Nantes cedex 03, France Tél : +33 251 125 636 - Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
