Dear Earl,
it looks like you might only need to add $RDBASE to your PYTHONPATH.
p.
On 13/03/2020 16:38, Earl Higgins wrote:
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 <module>
2: from rdkit.Chem import rdCoordGen, rdMolAlign
2: ModuleNotFoundError: No module named 'rdkit'
1/1 Test #2: pyCoordGen .......................***Failed 0.07 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 <paolo.tosco.m...@gmail.com>
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…
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