Dear Paolo,
> regarding test 13, would you mind trying to change line 1400 in
> /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp from [...]
> and tell me what the return value of
> MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) actually is?
The return value is -9 (is it a rounding error then?). This is the
full output from the test:
test 13
Start 13: testUFFForceField
13: Test command:
/home/M212767/RDKit/build/Code/ForceField/UFF/testUFFForceField
13: Test timeout computed to be: 9.99988e+06
13: -------------------------------------
13: Unit tests for force field basics.
13: done
13: -------------------------------------
13: Unit tests for basics of UFF bond-stretch terms.
13: done
13: -------------------------------------
13: Unit tests for UFF bond-stretch terms.
13: done
13: -------------------------------------
13: Unit tests for basics of UFF angle terms.
13: done
13: -------------------------------------
13: Unit tests for UFF angle-bend terms.
13: theta = 3.14159; theta0 = 3.14159
13: theta = 2.094395, param1.theta0 = 2.094395
13: done
13: -------------------------------------
13: Test Simple UFF molecule optimizations.
13: done
13: -------------------------------------
13: Unit tests for UFF nonbonded terms.
13: done
13: -------------------------------------
13: Test UFF torsional terms.
13: done
13: -------------------------------------
13: Test UFF Parameter objects
13: -------------------------------------
13: Test Simple UFF molecule optimization, part 2.
13: done
13: -------------------------------------
13: Test UFF Torsion Conflicts.
13: C 0.4783 -0.7477 -0.0753
13: C -0.5465 -0.0176 0.3519
13: C -0.5114 1.4472 0.0870
13: H -1.5201 -0.4838 0.2485
13: H 0.4696 1.8363 0.3367
13: O -1.2618 1.9423 0.6934
13: F -0.7163 1.6298 -0.9622
13: done
13: -------------------------------------
13: Unit tests for UFF distance constraint terms.
13: done
13: -------------------------------------
13: Unit tests for all UFF constraint terms.
13: -9
13: done
13: -------------------------------------
13: Unit tests for copying UFF ForceFields.
13: done
13/85 Test #13: testUFFForceField ................ Passed 0.35 sec
Best wishes,
Michal
On 17 March 2015 at 23:27, Paolo Tosco <[email protected]> wrote:
> Hi Michal,
>
> regarding test 13, would you mind trying to change line 1400 in
> /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp from
>
> TEST_ASSERT((int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6,
> 8) == -10);
>
> to
>
> std::cout << (int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3,
> 6, 8) << std::endl;
>
> and tell me what the return value of
> MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) actually is?
> It might just be a periodicity problem.
>
> Thanks for your collaboration, kind regards
> Paolo
>
>
> On 17/03/2015 14:48, Michal Krompiec wrote:
>>
>> Hello,
>> I'm trying to build RDKit on Cygwin, on Windows 7 32-bit (current
>> GitHub version).
>> So far, everything looked fine, but some tests failed:
>>
>> The following tests FAILED:
>> 13 - testUFFForceField (OTHER_FAULT)
>> 66 - testFMCS (SEGFAULT)
>> 79 - pythonTestDbCLI (Failed) - that's not a problem, as the
>> db is not set up (yet)
>>
>> I repeated using --output-on-failure, and that's what I got:
>>
>> testUFFForceField:
>> Test Assert
>> Expression Failed:
>> Violation occurred on line 1400 in file
>> /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp
>> Failed Expression:
>> (int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) ==
>> -10
>>
>> 66/85 Test #66: testFMCS .........................***Exception:
>> SegFault 0.28 sec
>> [14:16:12] *******************************************************
>> [14:16:12] FMCS Unit Test
>> [14:16:12] -------------------------------------
>> [14:16:12] FMCS test1Basics()
>>
>> System reboot and /bin/rebaseall did not help.
>>
>> Moreover, tests for the cartridge also failed:
>>
>> $ make && make install && make installcheck
>> make: Nothing to be done for 'all'.
>> /usr/bin/mkdir -p '/usr/lib/postgresql'
>> /usr/bin/mkdir -p '/usr/share/postgresql/extension'
>> /usr/bin/mkdir -p '/usr/share/postgresql/extension'
>> /usr/bin/install -c -m 755 rdkit.dll '/usr/lib/postgresql/rdkit.dll'
>> /usr/bin/install -c -m 644 rdkit.control
>> '/usr/share/postgresql/extension/'
>> /usr/bin/install -c -m 644 rdkit--3.4.sql
>> '/usr/share/postgresql/extension/'
>> /usr/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress
>> --inputdir=./ --psqldir='/usr/bin' --dbname=contrib_regression
>> rdkit-91 props btree molgist bfpgist-91 sfpgist slfpgist fps reaction
>> (using postmaster on Unix socket, default port)
>> ============== dropping database "contrib_regression" ==============
>> NOTICE: database "contrib_regression" does not exist, skipping
>> DROP DATABASE
>> ============== creating database "contrib_regression" ==============
>> CREATE DATABASE
>> ALTER DATABASE
>> ============== running regression test queries ==============
>> test rdkit-91 ... LOG: server process (PID 9076) was
>> terminated by signal 11: Segmentation fault
>> DETAIL: Failed process was running: CREATE EXTENSION rdkit;
>>
>> Has anybody else encountered such problems? Any idea what to do?
>>
>> Thanks,
>> Michal
>>
>>
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