[Debichem-devel] Openmm accepted but new version has build time test issues

[Andreas Tille]

Hi,

I've pushed the latest upstream version of openmm to Git to do a
source-only upload.  Unfortunately the build was running into:

...
/build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/gromacsgrofile.py:64
  /build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/gromacsgrofile.py:64: DeprecationWarning: invalid escape sequence \.
    return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word)

/build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/desmonddmsfile.py:411
  /build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/desmonddmsfile.py:411: SyntaxWarning: "is" with a literal. Did you mean "=="?
    if implicitSolvent is 'AGBNP3':

/build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/desmonddmsfile.py:433
  /build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/desmonddmsfile.py:433: SyntaxWarning: "is" with a literal. Did you mean "=="?
    if implicitSolvent is 'GVolSA':

/build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/desmonddmsfile.py:440
  /build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/desmonddmsfile.py:440: SyntaxWarning: "is" with a literal. Did you mean "=="?
    if implicitSolvent is 'AGBNP':

/build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/metadynamics.py:243
  /build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/metadynamics.py:243: DeprecationWarning: invalid escape sequence \.
    pattern = re.compile('bias_(.*)_(.*)\.npy')

TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes
TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent
TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces
TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters
  /build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/internal/amber_file_parser.py:1018: UserWarning: Non-optimal GB parameters detected for GB model GBn
    warnings.warn(

TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent
TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces
TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters
  /build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/internal/amber_file_parser.py:1018: UserWarning: Non-optimal GB parameters detected for GB model HCT
    warnings.warn(

TestForceField.py::TestForceField::test_ImpropersOrdering_smirnoff
  /build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM    2          A   1       0.513  -1.098  -0.004  1.00  0.00           O  , HETATM    1          A   1       0.095   0.011   0.000  1.00  0.00           C  )
    warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))

TestForceField.py::TestForceField::test_ImpropersOrdering_smirnoff
  /build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM    3          A   1      -1.098   0.149   0.015  1.00  0.00           H  , HETATM    2          A   1       0.513  -1.098  -0.004  1.00  0.00           O  )
    warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))

TestForceField.py::TestForceField::test_ImpropersOrdering_smirnoff
  /build/openmm-7.4.0.491.gac5a8f71+dfsg/obj-x86_64-linux-gnu/python/build/lib.linux-x86_64-3.8/simtk/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM    4          A   1       0.590   0.938  -0.011  1.00  0.00           H  , HETATM    3          A   1      -1.098   0.149   0.015  1.00  0.00           H  )
    warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))

-- Docs: https://docs.pytest.org/en/latest/warnings.html
======= 1 failed, 274 passed, 17 skipped, 29 warnings in 360.13 seconds ========
make[1]: *** [debian/rules:37: override_dh_auto_test] Error 1


I do not have time to track this down for the moment.

Kind regards

     Andreas.


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