Yes, it is definitely a rounding error, I will just have to make that check slightly more tolerant. For the time being, you may safely consider that test as passed.
Cheers, p. > On 18 Mar 2015, at 11:10, Michal Krompiec <[email protected]> wrote: > > 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 >>> >>> >>> ------------------------------------------------------------------------------ >>> Dive into the World of Parallel Programming The Go Parallel Website, >>> sponsored >>> by Intel and developed in partnership with Slashdot Media, is your hub for >>> all >>> things parallel software development, from weekly thought leadership blogs >>> to >>> news, videos, case studies, tutorials and more. Take a look and join the >>> conversation now. http://goparallel.sourceforge.net/ >>> _______________________________________________ >>> Rdkit-discuss mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
