Your message dated Thu, 19 Dec 2024 13:08:59 +0000
with message-id <[email protected]>
and subject line Bug#1090255: fixed in openmm 8.1.2+dfsg-2
has caused the Debian Bug report #1090255,
regarding openmm: FTBFS: UnicodeDecodeError: 'utf-8' codec can't decode byte
0xc4 in position 486: invalid continuation byte
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1090255: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1090255
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:openmm
Version: 8.1.2+dfsg-1
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary --buildsystem cmake --with numpy3,python3
dh_update_autotools_config -O--buildsystem=cmake
dh_autoreconf -O--buildsystem=cmake
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_C_FLAGS_RELEASE="-g
-O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_ENABLE_OPENMP"
-DCMAKE_CXX_FLAGS_RELEASE="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_ENABLE_OPENMP"
-DCMAKE_SHARED_LINKER_FLAGS_RELEASE="-Wl,-z,relro -Wl,--as-needed"
-DCMAKE_BUILD_RPATH_USE_ORIGIN=ON -DCMAKE_BUILD_TYPE=Release
-DOPENMM_BUILD_SERIALIZATION_SUPPORT=ON
-DOPENMM_BUILD_C_AND_FORTRAN_WRAPPERS=OFF -DOPENMM_BUILD_OPENCL_TESTS=OFF
cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb
PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr
-DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc
-DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON
-DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF
-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON
-DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run
-DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles"
-DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu
-DCMAKE_VERBOSE_MAKEFILE=ON "-DCMAKE_C_FLAGS_RELEASE=-g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_ENABLE_OPENMP"
"-DCMAKE_CXX_FLAGS_RELEASE=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_E
NABLE_OPENMP" "-DCMAKE_SHARED_LINKER_FLAGS_RELEASE=-Wl,-z,relro
-Wl,--as-needed" -DCMAKE_BUILD_RPATH_USE_ORIGIN=ON -DCMAKE_BUILD_TYPE=Release
-DOPENMM_BUILD_SERIALIZATION_SUPPORT=ON
-DOPENMM_BUILD_C_AND_FORTRAN_WRAPPERS=OFF -DOPENMM_BUILD_OPENCL_TESTS=OFF ..
CMake Warning (dev) at CMakeLists.txt:15 (find_package):
Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
are removed. Run "cmake --help-policy CMP0148" for policy details. Use
the cmake_policy command to set the policy and suppress this warning.
This warning is for project developers. Use -Wno-dev to suppress it.
[... snipped ...]
Test the CustomNonbondedForce generator ... ok
test_Cutoff (TestForceField.TestForceField.test_Cutoff)
Test to make sure the nonbondedCutoff parameter is passed correctly. ... ok
test_DispersionCorrection
(TestForceField.TestForceField.test_DispersionCorrection)
Test to make sure that the dispersion/long-range correction is set properly.
... ok
test_Disulfides (TestForceField.TestForceField.test_Disulfides)
Test that various force fields handle disulfides correctly. ... ok
test_DrudeMass (TestForceField.TestForceField.test_DrudeMass)
Test that setting the mass of Drude particles works correctly. ... ok
test_Forces (TestForceField.TestForceField.test_Forces)
Compute forces and compare them to ones generated with a previous version of
OpenMM to ensure they haven't changed. ... ok
test_Glycam (TestForceField.TestForceField.test_Glycam)
Test computing energy with GLYCAM. ... ok
test_HydrogenMass (TestForceField.TestForceField.test_HydrogenMass)
Test that altering the mass of hydrogens works correctly. ... ok
test_IdenticalTemplates (TestForceField.TestForceField.test_IdenticalTemplates)
Test a case where patches produce two identical templates. ... ok
test_IgnoreExternalBonds
(TestForceField.TestForceField.test_IgnoreExternalBonds)
Test the ignoreExternalBonds option ... ok
test_ImplicitSolvent (TestForceField.TestForceField.test_ImplicitSolvent)
Test the four types of implicit solvents using the implicitSolvent ... ok
test_ImplicitSolventForces
(TestForceField.TestForceField.test_ImplicitSolventForces)
Compute forces for different implicit solvent types, and compare them to ones
generated with AmberPrmtopFile. ... ok
test_ImplicitSolventParameters
(TestForceField.TestForceField.test_ImplicitSolventParameters)
Test that solventDielectric and soluteDielectric are passed correctly ... ok
test_ImpropersOrdering (TestForceField.TestForceField.test_ImpropersOrdering)
Test correctness of the ordering of atom indexes in improper torsions ... ok
test_ImpropersOrdering_smirnoff
(TestForceField.TestForceField.test_ImpropersOrdering_smirnoff)
Test correctness of the ordering of atom indexes in improper torsions ... ok
test_Includes (TestForceField.TestForceField.test_Includes)
Test using a ForceField that includes other files. ... ok
test_InitializationScript
(TestForceField.TestForceField.test_InitializationScript)
Test that <InitializationScript> tags get executed. ... ok
test_LennardJonesGenerator
(TestForceField.TestForceField.test_LennardJonesGenerator)
Test the LennardJones generator ... ok
test_MultipleFilesandForceTags
(TestForceField.TestForceField.test_MultipleFilesandForceTags)
Test that the order of listing of multiple ffxmls does not matter. ... ok
test_NBFix (TestForceField.TestForceField.test_NBFix)
Test using LennardJonesGenerator to implement NBFix terms. ... ok
test_NonbondedMethod (TestForceField.TestForceField.test_NonbondedMethod)
Test all six options for the nonbondedMethod parameter. ... ok
test_Opc3Energy (TestForceField.TestForceField.test_Opc3Energy) ... ok
test_OpcEnergy (TestForceField.TestForceField.test_OpcEnergy) ... ok
test_PeriodicBoxVectors (TestForceField.TestForceField.test_PeriodicBoxVectors)
Test setting the periodic box vectors. ... ok
test_ProgrammaticForceField
(TestForceField.TestForceField.test_ProgrammaticForceField)
Test building a ForceField programmatically. ... ok
test_RemoveCMMotion (TestForceField.TestForceField.test_RemoveCMMotion)
Test both options (True and False) for the removeCMMotion parameter. ... ok
test_ResidueAttributes (TestForceField.TestForceField.test_ResidueAttributes)
Test a ForceField that gets per-particle parameters from residue attributes.
... ok
test_ResidueOverriding (TestForceField.TestForceField.test_ResidueOverriding)
Test residue overriding via override tag in the XML ... ok
test_ResidueTemplateUserChoice
(TestForceField.TestForceField.test_ResidueTemplateUserChoice)
Test createSystem does not allow multiple matching templates, unless ... ok
test_RigidWaterAndConstraints
(TestForceField.TestForceField.test_RigidWaterAndConstraints)
Test all eight options for the constraints and rigidWater parameters. ... ok
test_ScalingFactorCombining
(TestForceField.TestForceField.test_ScalingFactorCombining)
Tests that FFs can be combined if their scaling factors are very close ... ok
test_SwitchingDistance (TestForceField.TestForceField.test_SwitchingDistance)
Test that the switchDistance parameter is processed correctly. ... ok
test_UnusedArgs (TestForceField.TestForceField.test_UnusedArgs)
Test that specifying an argument that is never used throws an exception. ... ok
test_Wildcard (TestForceField.TestForceField.test_Wildcard)
Test that PeriodicTorsionForces using wildcard ('') for atom types / classes in
the ffxml are correctly registered ... ok
test_flexibleConstraints
(TestForceField.TestForceField.test_flexibleConstraints)
Test the flexibleConstraints keyword ... ok
test_generateTemplatesForUnmatchedResidues
(TestForceField.TestForceField.test_generateTemplatesForUnmatchedResidues)
Test generation of blank forcefield residue templates for unmatched residues.
... ok
test_getMatchingTemplates
(TestForceField.TestForceField.test_getMatchingTemplates)
Test retrieval of list of templates that match residues in a topology. ... ok
test_getUnmatchedResidues
(TestForceField.TestForceField.test_getUnmatchedResidues)
Test retrieval of list of residues for which no templates are available. ... ok
test_residueMatcher (TestForceField.TestForceField.test_residueMatcher)
Test using a custom template matcher to select templates. ... ok
test_residueTemplateGenerator
(TestForceField.TestForceField.test_residueTemplateGenerator)
Test the ability to add residue template generators to parameterize unmatched
residues. ... ok
test1 (TestForceGroups.TestForceGroups.test1) ... ok
test2 (TestForceGroups.TestForceGroups.test2) ... ok
test3 (TestForceGroups.TestForceGroups.test3) ... ok
test_CustomHbondGenerator
(TestGenerators.TestGenerators.test_CustomHbondGenerator)
Test the generator for CustomHbondForce. ... ok
test_CustomHbondGenerator2
(TestGenerators.TestGenerators.test_CustomHbondGenerator2)
Test the generator for CustomHbondForce with different parameters. ... ok
test_Triclinic (TestGromacsGroFile.TestGromacsGroFile.test_Triclinic)
Test parsing a file that describes a triclinic box. ... ok
test_Cutoff (TestGromacsTopFile.TestGromacsTopFile.test_Cutoff)
Test to make sure the nonbondedCutoff parameter is passed correctly. ...
skipped 'GROMACS is not installed'
test_EwaldErrorTolerance
(TestGromacsTopFile.TestGromacsTopFile.test_EwaldErrorTolerance)
Test to make sure the ewaldErrorTolerance parameter is passed correctly. ...
skipped 'GROMACS is not installed'
test_GROMOS (TestGromacsTopFile.TestGromacsTopFile.test_GROMOS)
Test a system using the GROMOS 54a7 force field. ... skipped 'GROMACS is not
installed'
test_HydrogenMass (TestGromacsTopFile.TestGromacsTopFile.test_HydrogenMass)
Test that altering the mass of hydrogens works correctly. ... skipped 'GROMACS
is not installed'
test_NonbondedMethod
(TestGromacsTopFile.TestGromacsTopFile.test_NonbondedMethod)
Test all six options for the nonbondedMethod parameter. ... skipped 'GROMACS is
not installed'
test_RemoveCMMotion (TestGromacsTopFile.TestGromacsTopFile.test_RemoveCMMotion)
Test both options (True and False) for the removeCMMotion parameter. ...
skipped 'GROMACS is not installed'
test_RigidWaterAndConstraints
(TestGromacsTopFile.TestGromacsTopFile.test_RigidWaterAndConstraints)
Test all eight options for the constraints and rigidWater parameters. ...
skipped 'GROMACS is not installed'
test_SMOG (TestGromacsTopFile.TestGromacsTopFile.test_SMOG)
Test to ensure that SMOG models can be run without problems ... skipped
'GROMACS is not installed'
test_SwitchingFunction
(TestGromacsTopFile.TestGromacsTopFile.test_SwitchingFunction)
Test using a switching function. ... skipped 'GROMACS is not installed'
test_VirtualParticle
(TestGromacsTopFile.TestGromacsTopFile.test_VirtualParticle)
Test virtual particle works correctly. ... skipped 'GROMACS is not installed'
test_Vsite3 (TestGromacsTopFile.TestGromacsTopFile.test_Vsite3)
Test a three particle virtual site. ... skipped 'GROMACS is not installed'
test_ff99SBILDN (TestGromacsTopFile.TestGromacsTopFile.test_ff99SBILDN)
Test Gromacs topology #define replacement as used in ff99SB-ILDN ... skipped
'GROMACS is not installed'
test_ionic (TestGromacsTopFile.TestGromacsTopFile.test_ionic)
Test simulating an ionic liquid ... skipped 'GROMACS is not installed'
testBadGroups (TestIntegrators.TestIntegrators.testBadGroups)
Test the MTS integrator with bad force group substeps. ... ok
testDrudeNoseHooverIntegrator
(TestIntegrators.TestIntegrators.testDrudeNoseHooverIntegrator)
Test the DrudeNoseHooverIntegrator ... skipped 'Skipping test failing due to
missing platforms'
testMTSIntegratorConstraints
(TestIntegrators.TestIntegrators.testMTSIntegratorConstraints)
Test the MTS integrator energy conservation on a system of constrained
particles with no inner force (just constraints) ... ok
testMTSIntegratorExplicit
(TestIntegrators.TestIntegrators.testMTSIntegratorExplicit)
Test the MTS integrator on an explicit solvent system ... ok
testMTSLangevinIntegrator
(TestIntegrators.TestIntegrators.testMTSLangevinIntegrator)
Test the MTSLangevinIntegrator on an explicit solvent system ... ok
testMTSLangevinIntegratorFriction
(TestIntegrators.TestIntegrators.testMTSLangevinIntegratorFriction)
Test the MTSLangevinIntegrator on a force-free particle to ensure friction is
properly accounted for (issue #3790) ... ok
testNoseHooverIntegrator
(TestIntegrators.TestIntegrators.testNoseHooverIntegrator)
Test partial thermostating in the NoseHooverIntegrator (only API) ... ok
testHarmonicOscillator
(TestMetadynamics.TestMetadynamics.testHarmonicOscillator)
Test running metadynamics on a harmonic oscillator. ... ok
test_add (TestModeller.TestModeller.test_add)
Test the add() method. ... ok
test_addExtraParticles (TestModeller.TestModeller.test_addExtraParticles)
Test addExtraParticles(). ... ok
test_addHydrogensASH (TestModeller.TestModeller.test_addHydrogensASH)
Test of addHydrogens() in which we force ASH to be a variant using the variants
parameter. ... ok
test_addHydrogensCYX (TestModeller.TestModeller.test_addHydrogensCYX)
Test of addHydrogens() in which we force CYX to be a variant using the variants
parameter. ... ok
test_addHydrogensGLH (TestModeller.TestModeller.test_addHydrogensGLH)
Test of addHydrogens() in which we force GLH to be a variant using the variants
parameter. ... ok
test_addHydrogensGlycam (TestModeller.TestModeller.test_addHydrogensGlycam)
Test adding hydrogens for GLYCAM. ... ok
test_addHydrogensLYN (TestModeller.TestModeller.test_addHydrogensLYN)
Test of addHydrogens() in which we force LYN to be a variant using the variants
parameter. ... ok
test_addHydrogensPdb2 (TestModeller.TestModeller.test_addHydrogensPdb2)
Test the addHydrogens() method on the T4-lysozyme-L99A pdb file. ... ok
test_addHydrogensPdb3 (TestModeller.TestModeller.test_addHydrogensPdb3)
Test the addHydrogens() method on the metallothionein pdb file. ... ok
test_addHydrogensPdb3_keepPositions
(TestModeller.TestModeller.test_addHydrogensPdb3_keepPositions)
Test addHydrogens() does not change existing Hs positions ... ok
test_addHydrogenspH11 (TestModeller.TestModeller.test_addHydrogenspH11)
Test of addHydrogens() with pH=11. ... ok
test_addHydrogenspH4 (TestModeller.TestModeller.test_addHydrogenspH4)
Test of addHydrogens() with pH=4. ... ok
test_addHydrogenspH9 (TestModeller.TestModeller.test_addHydrogenspH9)
Test of addHydrogens() with pH=9. ... ok
test_addMembrane (TestModeller.TestModeller.test_addMembrane)
Test adding a membrane to a realistic system. ... skipped 'Skipping a test
which takes too long'
test_addSolventBoxShape (TestModeller.TestModeller.test_addSolventBoxShape)
Test the addSolvent() method; test the different box shapes. ... ok
test_addSolventIons (TestModeller.TestModeller.test_addSolventIons)
Test the addSolvent() method with all possible choices for positive and
negative ions. ... ok
test_addSolventNegativeSolvent
(TestModeller.TestModeller.test_addSolventNegativeSolvent)
Test the addSolvent() method; test adding ions to a negatively charged solvent.
... ok
test_addSolventNeutralSolvent
(TestModeller.TestModeller.test_addSolventNeutralSolvent)
Test the addSolvent() method; test adding ions to neutral solvent. ... ok
test_addSolventPeriodicBox
(TestModeller.TestModeller.test_addSolventPeriodicBox)
Test the addSolvent() method; test that the five ways of passing in the
periodic box all work. ... ok
test_addSolventPositiveSolvent
(TestModeller.TestModeller.test_addSolventPositiveSolvent)
Test the addSolvent() method; test adding ions to a positively charged solvent.
... ok
test_addSolventWaterModels
(TestModeller.TestModeller.test_addSolventWaterModels)
Test all addSolvent() method with all possible water models. ... ok
test_addVirtualSites (TestModeller.TestModeller.test_addVirtualSites)
Test adding extra particles defined by virtual sites. ... ok
test_convertWater (TestModeller.TestModeller.test_convertWater)
Test the convertWater() method. ... ok
test_delete (TestModeller.TestModeller.test_delete)
Test the delete() method. ... ok
test_deleteWater (TestModeller.TestModeller.test_deleteWater)
Test the deleteWater() method. ... ok
test_multiSiteIon (TestModeller.TestModeller.test_multiSiteIon)
Test adding extra particles whose positions are determined based on bonds. ...
ok
test_removeExtraHydrogens (TestModeller.TestModeller.test_removeExtraHydrogens)
Test that addHydrogens() can remove hydrogens that shouldn't be there. ... ok
test_CMAP (TestNumpyCompatibility.TestNumpyCompatibility.test_CMAP) ... ok
test_int64 (TestNumpyCompatibility.TestNumpyCompatibility.test_int64) ... ok
test_periodicBoxVectors
(TestNumpyCompatibility.TestNumpyCompatibility.test_periodicBoxVectors) ... ok
test_setPositions
(TestNumpyCompatibility.TestNumpyCompatibility.test_setPositions) ... ok
test_setPositions_units
(TestNumpyCompatibility.TestNumpyCompatibility.test_setPositions_units) ... ok
test_setVelocities
(TestNumpyCompatibility.TestNumpyCompatibility.test_setVelocities) ... ok
test_setVelocities_units
(TestNumpyCompatibility.TestNumpyCompatibility.test_setVelocities_units) ... ok
test_tabulatedFunction
(TestNumpyCompatibility.TestNumpyCompatibility.test_tabulatedFunction) ... ok
testNumpyAttributes (TestNumpyCompatibility.TestNumpyUnits.testNumpyAttributes)
... ok
testAlaAlaAla (TestPatches.TestPatches.testAlaAlaAla)
Test constructing a System that involves two patches. ... ok
testApplyPatch (TestPatches.TestPatches.testApplyPatch)
Test applying a patch to a template. ... ok
testDisulfidePatch (TestPatches.TestPatches.testDisulfidePatch) ... ok
testParseMultiresiduePatch (TestPatches.TestPatches.testParseMultiresiduePatch)
Test parsing a <Patch> tag that affects two residues. ... ok
testParsePatch (TestPatches.TestPatches.testParsePatch)
Test parsing a <Patch> tag. ... ok
test_AltLocs (TestPdbFile.TestPdbFile.test_AltLocs)
Test reading a file that includes AltLocs ... ok
test_BinaryStream (TestPdbFile.TestPdbFile.test_BinaryStream)
Test reading a stream that was opened in binary mode. ... ok
test_ExtraParticles (TestPdbFile.TestPdbFile.test_ExtraParticles)
Test reading, and writing and re-reading of a file containing extra particle
atoms. ... ok
test_LargeFile (TestPdbFile.TestPdbFile.test_LargeFile)
Write and read a file with more than 100,000 atoms ... ok
test_Triclinic (TestPdbFile.TestPdbFile.test_Triclinic)
Test parsing a file that describes a triclinic box. ... ok
test_WriteFile (TestPdbFile.TestPdbFile.test_WriteFile)
Write a file, read it back, and make sure it matches the original. ... ok
testBondSubset (TestPdbReporter.TestPDBReporter.testBondSubset)
Test that CONECT records are output correctly when using atomSubset ... ok
testInvalidSubsets (TestPdbReporter.TestPDBReporter.testInvalidSubsets)
Test that an exception is raised when the indices in atomSubset are invalid ...
ok
testSubset (TestPdbReporter.TestPDBReporter.testSubset)
Test writing out a subset of atoms ... ok
testWriteAll (TestPdbReporter.TestPDBReporter.testWriteAll)
Test all atoms are written when atomSubset is not specified ... ok
testBondSubset (TestPdbReporter.TestPDBxReporter.testBondSubset)
Test that struct_conn records are output correctly when using atomSubset ... ok
testInvalidSubsets (TestPdbReporter.TestPDBxReporter.testInvalidSubsets)
Test that an exception is raised when the indices in atomSubset are invalid ...
ok
testSubset (TestPdbReporter.TestPDBxReporter.testSubset)
Test writing out a subset of atoms ... ok
testWriteAll (TestPdbReporter.TestPDBxReporter.testWriteAll)
Test all atoms are written when atomSubset is not specified ... ok
testBonds (TestPdbxFile.TestPdbxFile.testBonds)
Test reading and writing a file that includes bonds. ... ok
testInsertionCodes (TestPdbxFile.TestPdbxFile.testInsertionCodes)
Test reading a file that uses insertion codes. ... ok
testMultiChain (TestPdbxFile.TestPdbxFile.testMultiChain)
Test reading and writing a file that includes multiple chains ... ok
testReporterExplicit (TestPdbxFile.TestPdbxFile.testReporterExplicit)
Tests the PDBxReporter with PBC ... ok
testReporterImplicit (TestPdbxFile.TestPdbxFile.testReporterImplicit)
Tests the PDBxReporter without PBC ... ok
test_FormatConversion (TestPdbxFile.TestPdbxFile.test_FormatConversion)
Test conversion from PDB to PDBx ... ok
test_Triclinic (TestPdbxFile.TestPdbxFile.test_Triclinic)
Test parsing a file that describes a triclinic box. ... ok
testCopyForce (TestPickle.TestPickle.testCopyForce)
Test copying a Python object whose class extends Force. ... ok
testCopyIntegrator (TestPickle.TestPickle.testCopyIntegrator)
Test copying a Python object whose class extends Integrator. ... ok
test_deepcopy (TestPickle.TestPickle.test_deepcopy)
Test that serialization/deserialization works (via deepcopy). ... ok
testHarmonicOscillator
(TestSimulatedTempering.TestSimulatedTempering.testHarmonicOscillator)
Test running simulated tempering on a harmonic oscillator. ... ok
testHarmonicOscillatorNPT
(TestSimulatedTempering.TestSimulatedTempering.testHarmonicOscillatorNPT)
Test running simulated tempering on a harmonic oscillator with a Monte Carlo
barostat. ... ok
testCheckpointing (TestSimulation.TestSimulation.testCheckpointing)
Test that checkpointing works correctly. ... ok
testLoadFromXML (TestSimulation.TestSimulation.testLoadFromXML)
Test creating a Simulation from XML files ... ok
testMinimizationReporter
(TestSimulation.TestSimulation.testMinimizationReporter)
Test invoking a reporter during minimization. ... ok
testRunForClockTime (TestSimulation.TestSimulation.testRunForClockTime)
Test the runForClockTime() method. ... ok
testSaveState (TestSimulation.TestSimulation.testSaveState)
Test that saving States works correctly. ... ok
testStep (TestSimulation.TestSimulation.testStep)
Test the step() method. ... ok
testWrappedCoordinates (TestSimulation.TestSimulation.testWrappedCoordinates)
Test generating reports with and without wrapped coordinates. ... ok
testAppend (TestStateDataReporter.TestStateDataReporter.testAppend)
Test appending to the StateDataReporter output. ...
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/tests/TestStateDataReporter.py:33:
ResourceWarning: unclosed file <_io.TextIOWrapper
name='/tmp/tmpsj_29swb/templog.txt' mode='r' encoding='UTF-8'>
lines = open(filename).read().split('\n')
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
test_1 (TestSwigWrappers.TestSwigWrappers.test_1) ... ok
test_bondtype_singleton (TestTopology.TestTopology.test_bondtype_singleton)
Tests that the bond types are really singletons ... ok
test_getters (TestTopology.TestTopology.test_getters)
Test getters for number of atoms, residues, chains. ... ok
test_residue_bonds (TestTopology.TestTopology.test_residue_bonds)
Test retrieving bonds for a residue produces expected results. ... ok
testComputePBCVectors (TestUnitCell.TestUnitCell.testComputePBCVectors)
Tests computing periodic box vectors ... ok
testReducePBCVectors (TestUnitCell.TestUnitCell.testReducePBCVectors)
Checks that reducePeriodicBoxVectors properly reduces vectors ... ok
testMultiplication (TestUnits.TestNumpyUnits.testMultiplication)
Tests that units override numpy.ndarray multiplication ... ok
testNumpyDeepCopy (TestUnits.TestNumpyUnits.testNumpyDeepCopy)
Check that deepcopy on numpy array does not strip units ... ok
testNumpyDivision (TestUnits.TestNumpyUnits.testNumpyDivision)
Tests that division of numpy Quantities works correctly ... ok
testNumpyFunctions (TestUnits.TestNumpyUnits.testNumpyFunctions)
Tests various numpy attributes that they result in Quantities ... ok
testNumpyIsString (TestUnits.TestNumpyUnits.testNumpyIsString)
Tests the internal _is_string method with numpy Quantities ... ok
testNumpyQuantity (TestUnits.TestNumpyUnits.testNumpyQuantity)
Tests that numpy arrays can form Quantity values ... ok
testAngleQuantities (TestUnits.TestUnits.testAngleQuantities)
Tests angle measurements ... ok
testBadQuantityComparisons (TestUnits.TestUnits.testBadQuantityComparisons)
Checks that comparisons of incompatible units fails ... ok
testBadQuantityConversions (TestUnits.TestUnits.testBadQuantityConversions)
Tests that conversions to incompatible units fails ... ok
testBadQuantityMaths (TestUnits.TestUnits.testBadQuantityMaths)
Tests that Maths of incompatible units properly fails ... ok
testBaseScaleMix (TestUnits.TestUnits.testBaseScaleMix)
Test mixing of BaseUnit and ScaledUnit instances ... ok
testBaseUnit (TestUnits.TestUnits.testBaseUnit)
Tests the creation of a base unit furlong ... ok
testCalorieConversion (TestUnits.TestUnits.testCalorieConversion)
Tests unit conversion with calories to joules ... ok
testChemistryProblems (TestUnits.TestUnits.testChemistryProblems)
Tests some gen-chem applications with Quantity's ... ok
testCollectionQuantities (TestUnits.TestUnits.testCollectionQuantities)
Tests the use of collections as Quantity values ... ok
testCollectionQuantityOperations
(TestUnits.TestUnits.testCollectionQuantityOperations)
Tests that Quantity collections behave correctly ... ok
testComparisonOperators (TestUnits.TestUnits.testComparisonOperators)
Tests unit comparison operators ... ok
testCompositeUnits (TestUnits.TestUnits.testCompositeUnits)
Tests the creation of a composite unit ... ok
testConversionFactorTo (TestUnits.TestUnits.testConversionFactorTo)
Tests the "conversion_factor_to" attribute of Units ... ok
testCreateNewBaseUnit (TestUnits.TestUnits.testCreateNewBaseUnit)
Tests creating a new base unit ... ok
testCreateNewScaledUnit (TestUnits.TestUnits.testCreateNewScaledUnit)
Tests creating a new ScaledUnit ... ok
testCreateNewUnit (TestUnits.TestUnits.testCreateNewUnit)
Tests creating a new Unit ... ok
testDimensionless (TestUnits.TestUnits.testDimensionless)
Tests the properties of unit.dimensionless ... ok
testGetUnitAttributes (TestUnits.TestUnits.testGetUnitAttributes)
Tests the unit attribute `getters' ... ok
testIllegalQuantityOps (TestUnits.TestUnits.testIllegalQuantityOps)
Test that illegal operations on Quantity objects fails ... ok
testIsCompatible (TestUnits.TestUnits.testIsCompatible)
Tests the is_compatible attribute of units ... ok
testIsQuantity (TestUnits.TestUnits.testIsQuantity)
Tests if is_quantity can detect Quantities vs. scalars and units ... ok
testIsUnit (TestUnits.TestUnits.testIsUnit)
Tests the unit.is_unit introspective function ... ok
testMisc (TestUnits.TestUnits.testMisc)
Miscellaneous tests for the unit package ... ok
testMutableQuantityOperations
(TestUnits.TestUnits.testMutableQuantityOperations)
Tests that mutable Quantity objects do not get unexpectedly changed ... ok
testPresetUnitSystems (TestUnits.TestUnits.testPresetUnitSystems)
Tests some of the pre-set UnitSystem's ... ok
testQuantityBadSqrt (TestUnits.TestUnits.testQuantityBadSqrt)
Tests that taking sqrt of Quantities with incompatible units fails ... ok
testQuantityCollectionMethods
(TestUnits.TestUnits.testQuantityCollectionMethods)
Tests some sequence methods on Quantity objects (no numpy) ... ok
testQuantityComparisons (TestUnits.TestUnits.testQuantityComparisons)
Tests binary comparison operators between Quantity ... ok
testQuantityComplicatedMaths (TestUnits.TestUnits.testQuantityComplicatedMaths)
Tests a complicated set of mathematical operations on a Quantity ... ok
testQuantityFormat (TestUnits.TestUnits.testQuantityFormat)
Tests the format method on Quantity instances ... ok
testQuantityMaths (TestUnits.TestUnits.testQuantityMaths)
Tests dimensional analysis & maths on and b/w Quantity objects ... ok
testQuantitySqrt (TestUnits.TestUnits.testQuantitySqrt)
Tests taking the square root of quantities ... ok
testReduceUnit (TestUnits.TestUnits.testReduceUnit)
Tests the reduce_unit functionality ... ok
testScalarQuantityConstructor
(TestUnits.TestUnits.testScalarQuantityConstructor)
Tests creating a Quantity using the Quantity constructor ... ok
testScalarQuantityMultiplyDivide
(TestUnits.TestUnits.testScalarQuantityMultiplyDivide)
Tests creating a scalar Quantity object by * or / by a Unit ... ok
testScaledUnit (TestUnits.TestUnits.testScaledUnit)
Tests ScaledUnit class with kilokelvins ... ok
testString (TestUnits.TestUnits.testString)
Tests unit handling with strings, which should be dimensionless ... ok
testToBaseUnit (TestUnits.TestUnits.testToBaseUnit)
Tests the "get_conversion_factor_to_base_units" method ... ok
testTruthiness (TestUnits.TestUnits.testTruthiness)
Tests the truthiness of units ... ok
testUnaryOperators (TestUnits.TestUnits.testUnaryOperators)
Tests unary operators on units ... ok
testUnitBadSqrt (TestUnits.TestUnits.testUnitBadSqrt)
Tests that illegal sqrt calls on incompatible units fails ... ok
testUnitDivision (TestUnits.TestUnits.testUnitDivision)
Tests the division of units and is_dimensionless ... ok
testUnitMathModule (TestUnits.TestUnits.testUnitMathModule)
Tests the unit_math functions on Quantity objects ... ok
testUnitMathModuleBadInput (TestUnits.TestUnits.testUnitMathModuleBadInput)
Tests that bad units to unit_math fails appropriately ... ok
testUnitSqrt (TestUnits.TestUnits.testUnitSqrt)
Tests taking the square root of units ... ok
testUnitString (TestUnits.TestUnits.testUnitString)
Test the Unit->str casting functionality ... ok
testUnitSystem (TestUnits.TestUnits.testUnitSystem)
Tests the creation of a UnitSystem and its behavior ... ok
testValueInUnit (TestUnits.TestUnits.testValueInUnit)
Tests the value_in_unit functionality for Quantity ... ok
testNegation (TestVec3.TestVectors.testNegation) ... ok
testVec3Addition (TestVec3.TestVectors.testVec3Addition) ... ok
testVec3Attributes (TestVec3.TestVectors.testVec3Attributes) ... ok
testVec3Division (TestVec3.TestVectors.testVec3Division) ... ok
testVec3Equality (TestVec3.TestVectors.testVec3Equality) ... ok
testVec3Multiplication (TestVec3.TestVectors.testVec3Multiplication) ... ok
testVec3Subtraction (TestVec3.TestVectors.testVec3Subtraction) ... ok
testAppend (TestXtcFile.TestXtcFile.testAppend)
Test appending to an existing trajectory. ... ok
testLongTrajectory (TestXtcFile.TestXtcFile.testLongTrajectory)
Test writing a trajectory that has more than 2^31 steps. ... ok
test_xtc_box_from_topology (TestXtcFile.TestXtcFile.test_xtc_box_from_topology)
Test the XTC file by writing a trajectory and reading it back. Letting the box
be set from the topology ... ok
test_xtc_cubic (TestXtcFile.TestXtcFile.test_xtc_cubic)
Test the XTC file by writing a trajectory and reading it back. Using a cubic
box ... ok
test_xtc_triclinic (TestXtcFile.TestXtcFile.test_xtc_triclinic)
Test the XTC file by writing a trajectory and reading it back. Using a
triclinic box ... ok
======================================================================
ERROR: test_NetCDF (TestAmberInpcrdFile.TestAmberInpcrdFile.test_NetCDF)
Test NetCDF restart file parsing
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/openmm/app/internal/amber_file_parser.py",
line 1443, in __init__
from scipy.io import NetCDFFile
ImportError: cannot import name 'NetCDFFile' from 'scipy.io'
(/usr/lib/python3/dist-packages/scipy/io/__init__.py)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/openmm/app/internal/amber_file_parser.py",
line 1447, in __init__
from scipy.io.netcdf import NetCDFFile
ImportError: cannot import name 'NetCDFFile' from 'scipy.io.netcdf'
(/usr/lib/python3/dist-packages/scipy/io/netcdf.py)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/openmm/app/internal/amber_file_parser.py",
line 1537, in readAmberCoordinates
crdfile = AmberNetcdfRestart(filename)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/openmm/app/internal/amber_file_parser.py",
line 1449, in __init__
raise ImportError('scipy is necessary to parse NetCDF '
ImportError: scipy is necessary to parse NetCDF restarts
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/openmm/app/internal/amber_file_parser.py",
line 1541, in readAmberCoordinates
crdfile = AmberAsciiRestart(filename)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/openmm/app/internal/amber_file_parser.py",
line 1261, in __init__
lines = f.readlines()
^^^^^^^^^^^^^
File "<frozen codecs>", line 322, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc4 in position 486:
invalid continuation byte
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/tests/TestAmberInpcrdFile.py",
line 43, in test_NetCDF
inpcrd = AmberInpcrdFile('systems/amber.ncrst')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/openmm/app/amberinpcrdfile.py",
line 81, in __init__
results = amber_file_parser.readAmberCoordinates(file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/openmm/app/internal/amber_file_parser.py",
line 1547, in readAmberCoordinates
raise TypeError('Could not parse Amber ASCII restart file %s' %
TypeError: Could not parse Amber ASCII restart file systems/amber.ncrst
----------------------------------------------------------------------
Ran 327 tests in 533.463s
FAILED (errors=1, skipped=21)
#"Steps" "Temperature (K)" "200K Weight" "216.012K Weight"
"233.306K Weight" "251.984K Weight" "272.158K Weight"
"293.947K Weight" "317.48K Weight" "342.898K Weight"
"370.35K Weight" "400K Weight"
10000 216.012 0 -0.132812 -0.179688 -0.132812
-0.117188 -0.1875 -0.3125 -0.421875 -0.289062 -0.375
20000 293.947 0 -0.1026 -0.166138 -0.144348 -0.0971069
-0.138428 -0.307617 -0.328857 -0.265442 -0.372742
30000 272.158 0 -0.102161 -0.16566 -0.144083
-0.0975018 -0.138473 -0.30751 -0.328107 -0.264848
-0.372345
40000 272.158 0 -0.102154 -0.165653 -0.144075
-0.0975018 -0.138476 -0.307503 -0.3281 -0.26484
-0.372337
50000 272.158 0 -0.102154 -0.165653 -0.144075
-0.0975019 -0.138476 -0.307503 -0.3281 -0.26484
-0.372337
60000 251.984 0 -0.102154 -0.165653 -0.144075
-0.0975019 -0.138476 -0.307503 -0.3281 -0.26484
-0.372337
70000 317.48 0 -0.102154 -0.165653 -0.144075
-0.0975019 -0.138476 -0.307503 -0.3281 -0.26484
-0.372337
80000 251.984 0 -0.102154 -0.165653 -0.144075
-0.0975019 -0.138476 -0.307503 -0.3281 -0.26484
-0.372337
90000 216.012 0 -0.102154 -0.165653 -0.144075
-0.0975019 -0.138476 -0.307503 -0.3281 -0.26484
-0.372337
100000 216.012 0 -0.102154 -0.165653 -0.144075
-0.0975019 -0.138476 -0.307503 -0.3281 -0.26484
-0.372337
110000 216.012 0 -0.102154 -0.165653 -0.144075
-0.0975019 -0.138476 -0.307503 -0.3281 -0.26484
-0.372337
#"Steps" "Temperature (K)" "200K Weight" "216.012K Weight"
"233.306K Weight" "251.984K Weight" "272.158K Weight"
"293.947K Weight" "317.48K Weight" "342.898K Weight"
"370.35K Weight" "400K Weight"
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build; python3.12 -m unittest discover
-v --start-directory tests -p 'Test*'
make[1]: *** [debian/rules:45: override_dh_auto_test] Error 13
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:35: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202412/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
--- End Message ---
--- Begin Message ---
Source: openmm
Source-Version: 8.1.2+dfsg-2
Done: Andrius Merkys <[email protected]>
We believe that the bug you reported is fixed in the latest version of
openmm, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <[email protected]> (supplier of updated openmm package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 19 Dec 2024 07:43:03 -0500
Source: openmm
Architecture: source
Version: 8.1.2+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1090255
Changes:
openmm (8.1.2+dfsg-2) unstable; urgency=medium
.
* Backport upstream PR to restore compatibility with scipy
(Closes: #1090255).
Checksums-Sha1:
64a20ad557e0f796892db75d3580959e4ba1da66 2508 openmm_8.1.2+dfsg-2.dsc
5b92063266c6f7870e7a8185aa28bb4c73c4cdc5 19676
openmm_8.1.2+dfsg-2.debian.tar.xz
1bcfb8caa02a5f851bc4541f9abca2ba22493c62 10669
openmm_8.1.2+dfsg-2_source.buildinfo
Checksums-Sha256:
d2ae11804fe227d5acd6b73f497bce49244fcce449189f15abaed9ebf7a3a822 2508
openmm_8.1.2+dfsg-2.dsc
c226bc41aeee48239fda37ad4f8265e1fc7fa436d6901a71e8a6e2ac4ba86b56 19676
openmm_8.1.2+dfsg-2.debian.tar.xz
46348f2296383b703b37b9d319eaf9e191a6de6ce5c2e3a3555d7b9d97b71158 10669
openmm_8.1.2+dfsg-2_source.buildinfo
Files:
ff9a7f9533b1c20ac581339036f5edb4 2508 libs optional openmm_8.1.2+dfsg-2.dsc
dda6925c4c90ea4b453d5a8cdda8d4a8 19676 libs optional
openmm_8.1.2+dfsg-2.debian.tar.xz
7130de6b40c04373519e941fe8cf76bf 10669 libs optional
openmm_8.1.2+dfsg-2_source.buildinfo
-----BEGIN PGP SIGNATURE-----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=T+al
-----END PGP SIGNATURE-----
pgpJdg902rOj9.pgp
Description: PGP signature
--- End Message ---
