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
under Ubuntu 18.04.4 LTS running in a VM using Oracle VirtualBox (host
Windows 10). I need to be able to build from source because, as a
developer, I am on a team which is looking at making some enhancements
to the MOL file load support, possibly adding support for Opensmiles
as a distinct dialect of SMILES.
So, following the Linux/Python 3 instructions at
https://www.rdkit.org/docs/Install.html#how-to-build-from-source-with-conda
, I am able to download and install everything fine until I get to the
step to run ctest. I get:
$ ctest
CMake Error at /home/deep/conda-rdkit/rdkit/build/CTestCustom.ctest:3
(MESSAGE):
Please set your RDBASE env variable before running the tests.
Problem reading custom configuration:
/home/deep/conda-rdkit/rdkit/build/CTestCustom.ctest
Test project /home/deep/conda-rdkit/rdkit/build
No tests were found!!!
$
So I run:
$ RDBASE=~/conda-rdkit/rdkit ctest
When I do that, I get:
$ RDBASE=~/conda-rdkit/rdkit ctest
Test project /home/deep/conda-rdkit/rdkit/build
Start 1: testCoordGen
1/165 Test #1: testCoordGen ...........................
Passed 0.37 sec
Start 2: pyCoordGen
2/165 Test #2: pyCoordGen
.............................***Failed 0.05 sec
Start 3: testDict
3/165 Test #3: testDict ...............................
Passed 0.63 sec
Start 4: testRDValue
4/165 Test #4: testRDValue ............................
Passed 0.00 sec
Start 5: testDataStructs
5/165 Test #5: testDataStructs ........................
Passed 0.01 sec
Start 6: testFPB
6/165 Test #6: testFPB ................................
Passed 0.01 sec
Start 7: testMultiFPB
7/165 Test #7: testMultiFPB ...........................
Passed 0.04 sec
Start 8: pyBV
8/165 Test #8: pyBV
...................................***Failed 0.05 sec
Start 9: pyDiscreteValueVect
9/165 Test #9: pyDiscreteValueVect
....................***Failed 0.09 sec
Start 10: pySparseIntVect
10/165 Test #10: pySparseIntVect ........................***Failed
0.06 sec
Start 11: pyFPB
11/165 Test #11: pyFPB ..................................***Failed
0.05 sec
Start 12: testTransforms
12/165 Test #12: testTransforms ......................... Passed
0.01 sec
Start 13: testGrid
13/165 Test #13: testGrid ............................... Passed
0.04 sec
Start 14: geometryTestsCatch
(Lines omitted)
161/165 Test #161: pythonTestDirDbase
.....................***Failed 0.03 sec
Start 162: pythonTestDirSimDivFilters
162/165 Test #162: pythonTestDirSimDivFilters
.............***Failed 0.04 sec
Start 163: pythonTestDirVLib
163/165 Test #163: pythonTestDirVLib
......................***Failed 0.04 sec
Start 164: pythonTestDirChem
164/165 Test #164: pythonTestDirChem
......................***Failed 0.06 sec
Start 165: pythonTestSping
165/165 Test #165: pythonTestSping
........................***Failed 0.03 sec
47% tests passed, 87 tests failed out of 165
Total Test time (real) = 48.62 sec
The following tests FAILED:
2 - pyCoordGen (Failed)
8 - pyBV (Failed)
9 - pyDiscreteValueVect (Failed)
10 - pySparseIntVect (Failed)
11 - pyFPB (Failed)
15 - testPyGeometry (Failed)
19 - pyAlignment (Failed)
22 - testMMFFForceField (Child aborted)
23 - pyForceFieldConstraints (Failed)
25 - pyDistGeom (Failed)
28 - graphmolqueryTest (Child aborted)
29 - graphmolMolOpsTest (Child aborted)
31 - graphmoltestPickler (Child aborted)
34 - hanoiTest (Child aborted)
(Lines omitted)
157 - pyFeatures (Failed)
158 - pythonTestDbCLI (Failed)
159 - pythonTestDirML (Failed)
160 - pythonTestDirDataStructs (Failed)
161 - pythonTestDirDbase (Failed)
162 - pythonTestDirSimDivFilters (Failed)
163 - pythonTestDirVLib (Failed)
164 - pythonTestDirChem (Failed)
165 - pythonTestSping (Failed)
Errors while running CTest
$
My impression is RDKit is quite robust, well tested and portable and
I'm surprised at 87/165 test case failures right out of the box. I'm
very comfortable with the UNIX environment, bash command line,
makefiles, compiling and linking C and C++ software, so I don't think
I'm making any silly newbie mistakes.
Perhaps it's my unfamiliarity with Anaconda, cmake and specifically
the ctest utility, but it is unclear to me how I can get further
information about the cause of each of the 87 test case failures. Do I
need to connect with the my.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
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