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branch: master 「№59596」
Commited by: Andrew Watkins
GitHub commit link: 「8a21c04b5d692936」
Difference from previous tested commit:  code diff
Commit date: 2017-07-19 22:26:57
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug mac.cxx11thread OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tutorials integration.valgrind integration maintenance.documentation performance profile linux.clang.python2.release.PyRosetta4.Debug linux.clang.python3.release.PyRosetta4.Debug mac.clang.python3.5.release.PyRosetta4.Debug ubuntu.clang.python2.release.PyRosetta4.Debug mac.clang.python2.7.release.PyRosetta4.MinSizeRel mac.clang.python3.5.release.PyRosetta4.MinSizeRel linux.clang.python2.release.PyRosetta4.Release linux.clang.python3.release.PyRosetta4.Release mac.clang.python2.7.release.PyRosetta4.Release mac.clang.python3.5.release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score unit.ubsan

Merge pull request #2390 from RosettaCommons/everyday847/full_model_jq Make jd3 versions of common RNA applications

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Test: linux.gcc.code_quality.beautification

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/apps/public/darc/DARC.cc src/apps/public/pepspec/pepspec.cc src/apps/public/pepspec/pepspec_anchor_dock.cc src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc src/apps/public/weight_optimization/torsional_potential_corrections.cc src/core/conformation/UltraLightResidue.cc src/core/conformation/symmetry/SymmetryInfo.cc src/core/io/silent/RNA_SilentStruct.cc src/core/optimization/Minimizer.cc src/core/pack/rotamers/SingleNCAARotamerLibraryCreator.cc src/core/scoring/ResidualDipolarCoupling.cc src/core/scoring/constraints/BigBinConstraint.cc src/core/scoring/constraints/ConstraintIO.cc src/core/scoring/dna/base_geometry.cc src/core/scoring/dssp/StrandPairing.cc src/core/scoring/facts/FACTSPotential.cc src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc src/core/scoring/membrane/MPEnvEnergy.cc src/core/scoring/methods/GaussianOverlapEnergy.cc src/core/scoring/methods/MembraneEnvSmoothEnergy.cc src/core/scoring/methods/ResidualDipolarCouplingEnergy_Rohl.cc src/core/scoring/orbitals/OrbitalsScore.cc src/core/scoring/packing/PoseBalls.cc src/core/scoring/power_diagram/PowerDiagram.cc src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc src/core/select/residue_selector/GlycanPositionSelector.cc src/devel/denovo_protein_design/DesignRelaxMover.cc src/devel/splice/Splice.cc src/protocols/antibody/AntibodyInfo.cc src/protocols/antibody/ModelCDRH3.cc src/protocols/cartesian/md.cc src/protocols/comparative_modeling/LoopRelaxMover.cc src/protocols/cryst/refinable_lattice.cc src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc src/protocols/denovo_design/components/SheetDB.cc src/protocols/enzdes/EnzdesFlexBBProtocol.cc src/protocols/enzdes/SecondaryMatchProtocol.cc src/protocols/enzdes/enzdes_util.cc src/protocols/forge/remodel/RemodelAccumulator.cc src/protocols/frag_picker/scores/PhiPsiRmsd.cc src/protocols/frags/TorsionFragment.cc src/protocols/hybridization/FragmentBiasAssigner.cc src/protocols/hybridization/TMalign.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loophash/LoopHashLibrary.cc src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc src/protocols/loops/loops_main.cc src/protocols/make_rot_lib/MakeRotLib.cc src/protocols/make_rot_lib/MakeRotLibMover.cc src/protocols/membrane/OptimizeMembranePositionMover.cc src/protocols/metal_interface/FindClosestAtom.cc src/protocols/moves/MoverStatus.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refinement.cc src/protocols/mpi_refinement/MultiObjective.cc src/protocols/mpi_refinement/util.cc src/protocols/noesy_assign/PeakFileFormat.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/pockets/Fingerprint.cc src/protocols/pockets/PocketGrid.cc src/protocols/rna/denovo/fragments/FullAtomRNA_Fragments.cc src/protocols/rna/movers/ErraserMinimizerMover.cc src/protocols/scoring/ImplicitFastClashCheck.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/sewing/sampling/MonteCarloAssemblyMover.cc src/protocols/simple_filters/ResidueIEFilter.cc src/protocols/simple_filters/SheetFilter.cc src/protocols/simple_moves/AddCavitiesMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/sparta/Sparta.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.cc src/protocols/stepwise/modeler/util.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/viewer/triangleIterator.cc src/utility/libsvm/Svm.cc test/core/conformation/UltraLightResidue.cxxtest.hh


branch: master 「№59595」
Commited by: Brandon Frenz
GitHub commit link: 「44e1f4d47ba4dc0d」
Difference from previous tested commit:  code diff
Commit date: 2017-07-18 21:42:49
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python3.PyRosetta4.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug mac.cxx11thread OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration.tutorials integration maintenance.documentation performance profile linux.clang.python3.release.PyRosetta4.Debug mac.clang.python2.7.release.PyRosetta4.Debug ubuntu.clang.python3.release.PyRosetta4.Debug linux.clang.python2.release.PyRosetta4.MinSizeRel linux.clang.python3.release.PyRosetta4.MinSizeRel mac.clang.python3.5.release.PyRosetta4.MinSizeRel mac.clang.python2.7.release.PyRosetta4.Release mac.clang.python3.5.release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score unit.valgrind

Merge pull request #2400 from RosettaCommons/bfrenz/maintain_sugar_names Bfrenz/maintain sugar names



branch: master 「№59594」
Commited by: Rocco Moretti
GitHub commit link: 「ab5b5bd1f62c7367」
Difference from previous tested commit:  code diff
Commit date: 2017-07-18 19:06:41
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score

Merge pull request #2395 from RosettaCommons/roccomoretti/jd2ectomy Laying the groundwork for a jd2-ectomy A number of people have made use of the JD2 system when writing their Movers, etc. -- that is, they're not implementing something that has a direct dependence on JD2, but use various convenience functions in JD2 which allows you get various job-running data (e.g. output name) This has worked for the past decade or so, but now that JD3 is staring us in the face, it would be good to move such code off of a strict JD2-dependency. This PR goes through and, as much as reasonably possible, attempts to remove the direct dependence on JD2 Jobs, JobDistributors, JobOutputters, etc. from everywhere that's not intimately tied to the JD2 system. The form this takes in the current PR is that a number of utility functions have been added to src/protocols/jd2/util.hh, so instead of doing something like protocols::jd2::JobDistributor::get_instance()->current_job()->input_tag() you can do protocols::jd2::current_input_tag(). While the implementation of protocols::jd2::current_input_tag() still has the same reliance on the JD2 system, it serves as a single point which can be generalized when we come up with a JD2-independent system for passing around the input tag. (It should also be easier to mode it to a different namespace.)



branch: master 「№59593」
Commited by: Rocco Moretti
GitHub commit link: 「fe37478bd1ee69d9」
Difference from previous tested commit:  code diff
Commit date: 2017-07-17 16:47:37
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python3.PyRosetta4.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration performance profile linux.clang.python2.release.PyRosetta4.Debug linux.clang.python3.release.PyRosetta4.Debug mac.clang.python2.7.release.PyRosetta4.Debug mac.clang.python3.5.release.PyRosetta4.Debug linux.clang.python2.release.PyRosetta4.MinSizeRel linux.clang.python3.release.PyRosetta4.MinSizeRel mac.clang.python2.7.release.PyRosetta4.MinSizeRel mac.clang.python3.5.release.PyRosetta4.MinSizeRel ubuntu.clang.python2.release.PyRosetta4.MinSizeRel ubuntu.clang.python3.release.PyRosetta4.MinSizeRel linux.clang.python2.release.PyRosetta4.Release linux.clang.python3.release.PyRosetta4.Release mac.clang.python2.7.release.PyRosetta4.Release mac.clang.python3.5.release.PyRosetta4.Release ubuntu.clang.python2.release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score

Merge pull request #2396 from RosettaCommons/roccomoretti/fix_talaris_warning Fix issue where 'pre_talaris_2013_standard' was being classified as a talaris scorefunction.

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/apps/public/darc/DARC.cc src/apps/public/pepspec/pepspec.cc src/apps/public/pepspec/pepspec_anchor_dock.cc src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc src/apps/public/weight_optimization/torsional_potential_corrections.cc src/core/conformation/UltraLightResidue.cc src/core/conformation/symmetry/SymmetryInfo.cc src/core/io/silent/RNA_SilentStruct.cc src/core/optimization/Minimizer.cc src/core/pack/rotamers/SingleNCAARotamerLibraryCreator.cc src/core/scoring/ResidualDipolarCoupling.cc src/core/scoring/constraints/BigBinConstraint.cc src/core/scoring/constraints/ConstraintIO.cc src/core/scoring/dna/base_geometry.cc src/core/scoring/dssp/StrandPairing.cc src/core/scoring/facts/FACTSPotential.cc src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc src/core/scoring/membrane/MPEnvEnergy.cc src/core/scoring/methods/GaussianOverlapEnergy.cc src/core/scoring/methods/MembraneEnvSmoothEnergy.cc src/core/scoring/methods/ResidualDipolarCouplingEnergy_Rohl.cc src/core/scoring/orbitals/OrbitalsScore.cc src/core/scoring/packing/PoseBalls.cc src/core/scoring/power_diagram/PowerDiagram.cc src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc src/core/select/residue_selector/GlycanPositionSelector.cc src/devel/denovo_protein_design/DesignRelaxMover.cc src/devel/splice/Splice.cc src/protocols/antibody/AntibodyInfo.cc src/protocols/antibody/ModelCDRH3.cc src/protocols/cartesian/md.cc src/protocols/comparative_modeling/LoopRelaxMover.cc src/protocols/cryst/refinable_lattice.cc src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc src/protocols/denovo_design/components/SheetDB.cc src/protocols/enzdes/EnzdesFlexBBProtocol.cc src/protocols/enzdes/SecondaryMatchProtocol.cc src/protocols/enzdes/enzdes_util.cc src/protocols/forge/remodel/RemodelAccumulator.cc src/protocols/frag_picker/scores/PhiPsiRmsd.cc src/protocols/frags/TorsionFragment.cc src/protocols/hybridization/FragmentBiasAssigner.cc src/protocols/hybridization/TMalign.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loophash/LoopHashLibrary.cc src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc src/protocols/loops/loops_main.cc src/protocols/make_rot_lib/MakeRotLib.cc src/protocols/make_rot_lib/MakeRotLibMover.cc src/protocols/membrane/OptimizeMembranePositionMover.cc src/protocols/metal_interface/FindClosestAtom.cc src/protocols/moves/MoverStatus.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refinement.cc src/protocols/mpi_refinement/MultiObjective.cc src/protocols/mpi_refinement/util.cc src/protocols/noesy_assign/PeakFileFormat.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/pockets/Fingerprint.cc src/protocols/pockets/PocketGrid.cc src/protocols/rna/denovo/fragments/FullAtomRNA_Fragments.cc src/protocols/rna/movers/ErraserMinimizerMover.cc src/protocols/scoring/ImplicitFastClashCheck.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/sewing/sampling/MonteCarloAssemblyMover.cc src/protocols/simple_filters/ResidueIEFilter.cc src/protocols/simple_filters/SheetFilter.cc src/protocols/simple_moves/AddCavitiesMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/sparta/Sparta.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.cc src/protocols/stepwise/modeler/util.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/viewer/triangleIterator.cc src/utility/libsvm/Svm.cc test/core/conformation/UltraLightResidue.cxxtest.hh


branch: master 「№59592」
Commited by: Brandon Frenz
GitHub commit link: 「06c0359434044773」
Difference from previous tested commit:  code diff
Commit date: 2017-07-17 14:51:48
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score

Merge pull request #2383 from RosettaCommons/bfrenz/auto_glycan_with_links_records Bfrenz/auto glycan with links records

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Test: mac.clang.integration

Failed sub-tests (click for more details):
bundlegridsampler_epsilon
Test: linux.gcc.performance

Failed sub-tests (click for more details):
protocols_docking_DockingLowRes


branch: master 「№59591」
Commited by: Vikram K. Mulligan
GitHub commit link: 「fa91853df5aabfa2」
Difference from previous tested commit:  code diff
Commit date: 2017-07-15 02:13:10
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python3.PyRosetta4.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tutorials integration.valgrind integration maintenance.documentation performance profile linux.clang.python2.release.PyRosetta4.Debug linux.clang.python3.release.PyRosetta4.Debug mac.clang.python2.7.release.PyRosetta4.Debug mac.clang.python3.5.release.PyRosetta4.Debug linux.clang.python2.release.PyRosetta4.MinSizeRel linux.clang.python3.release.PyRosetta4.MinSizeRel mac.clang.python2.7.release.PyRosetta4.MinSizeRel mac.clang.python3.5.release.PyRosetta4.MinSizeRel linux.clang.python2.release.PyRosetta4.Release linux.clang.python3.release.PyRosetta4.Release mac.clang.python2.7.release.PyRosetta4.Release mac.clang.python3.5.release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score unit.addsan unit.valgrind

Merge pull request #2397 from RosettaCommons/vmullig/fix_link_issue Fixing a minor issue with using simple_cycpep_predict with native PDB files containing LINK records Requested by @gbhardwaj . When provided with a native structure with a LINK record specifying cyclic geometry, simple_cycpep_predict would attempt to set up cyclic geometry anew, first stripping off terminal types. When the terminal types were absent, it would crash. This fixes that.

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/apps/public/darc/DARC.cc src/apps/public/pepspec/pepspec.cc src/apps/public/pepspec/pepspec_anchor_dock.cc src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc src/apps/public/weight_optimization/torsional_potential_corrections.cc src/core/conformation/UltraLightResidue.cc src/core/conformation/symmetry/SymmetryInfo.cc src/core/io/silent/RNA_SilentStruct.cc src/core/optimization/Minimizer.cc src/core/pack/rotamers/SingleNCAARotamerLibraryCreator.cc src/core/scoring/ResidualDipolarCoupling.cc src/core/scoring/constraints/BigBinConstraint.cc src/core/scoring/constraints/ConstraintIO.cc src/core/scoring/dna/base_geometry.cc src/core/scoring/dssp/StrandPairing.cc src/core/scoring/facts/FACTSPotential.cc src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc src/core/scoring/membrane/MPEnvEnergy.cc src/core/scoring/methods/GaussianOverlapEnergy.cc src/core/scoring/methods/MembraneEnvSmoothEnergy.cc src/core/scoring/methods/ResidualDipolarCouplingEnergy_Rohl.cc src/core/scoring/orbitals/OrbitalsScore.cc src/core/scoring/packing/PoseBalls.cc src/core/scoring/power_diagram/PowerDiagram.cc src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc src/core/select/residue_selector/GlycanPositionSelector.cc src/devel/denovo_protein_design/DesignRelaxMover.cc src/devel/splice/Splice.cc src/protocols/antibody/AntibodyInfo.cc src/protocols/antibody/ModelCDRH3.cc src/protocols/cartesian/md.cc src/protocols/comparative_modeling/LoopRelaxMover.cc src/protocols/cryst/refinable_lattice.cc src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc src/protocols/denovo_design/components/SheetDB.cc src/protocols/enzdes/EnzdesFlexBBProtocol.cc src/protocols/enzdes/SecondaryMatchProtocol.cc src/protocols/enzdes/enzdes_util.cc src/protocols/forge/remodel/RemodelAccumulator.cc src/protocols/frag_picker/scores/PhiPsiRmsd.cc src/protocols/frags/TorsionFragment.cc src/protocols/hybridization/FragmentBiasAssigner.cc src/protocols/hybridization/TMalign.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loophash/LoopHashLibrary.cc src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc src/protocols/loops/loops_main.cc src/protocols/make_rot_lib/MakeRotLib.cc src/protocols/make_rot_lib/MakeRotLibMover.cc src/protocols/membrane/OptimizeMembranePositionMover.cc src/protocols/metal_interface/FindClosestAtom.cc src/protocols/moves/MoverStatus.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refinement.cc src/protocols/mpi_refinement/MultiObjective.cc src/protocols/mpi_refinement/util.cc src/protocols/noesy_assign/PeakFileFormat.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/pockets/Fingerprint.cc src/protocols/pockets/PocketGrid.cc src/protocols/rna/denovo/fragments/FullAtomRNA_Fragments.cc src/protocols/rna/movers/ErraserMinimizerMover.cc src/protocols/scoring/ImplicitFastClashCheck.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/sewing/sampling/MonteCarloAssemblyMover.cc src/protocols/simple_filters/ResidueIEFilter.cc src/protocols/simple_filters/SheetFilter.cc src/protocols/simple_moves/AddCavitiesMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/sparta/Sparta.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.cc src/protocols/stepwise/modeler/util.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/viewer/triangleIterator.cc src/utility/libsvm/Svm.cc test/core/conformation/UltraLightResidue.cxxtest.hh
Test: linux.gcc.performance

Failed sub-tests (click for more details):
core_import_pose_pose_from_pdbstring core_pack_linmem_ig_mmstd core_pack_linmem_ig_sc12he core_pack_linmem_ig_sc12sp2 core_pack_linmem_ig_score12 core_scoring_Score_10000x_cbeta core_scoring_Score_10000x_cbeta_smooth core_scoring_Score_10000x_cen_env_smooth core_scoring_Score_10000x_dslf_fa13 core_scoring_Score_10000x_omega core_scoring_Score_10000x_rama core_scoring_Score_10000x_rama2b core_scoring_Score_10000x_yhh_planarity core_scoring_Score_1000x_dslf_cbs_ds core_scoring_Score_1000x_mm_stretch core_scoring_Score_1000x_p_aa_pp core_scoring_Score_100x_cart_bonded core_scoring_Score_100x_cen_pair_smooth core_scoring_Score_100x_cenpack core_scoring_Score_100x_cenpack_smooth core_scoring_Score_100x_ch_bond core_scoring_Score_100x_envsmooth core_scoring_Score_100x_fa_cust_pair_dist core_scoring_Score_100x_fa_dun core_scoring_Score_100x_fa_dun_dev core_scoring_Score_100x_fa_dun_rot core_scoring_Score_100x_fa_dun_semi core_scoring_Score_100x_fa_pair core_scoring_Score_100x_fa_pair_aro_aro core_scoring_Score_100x_fa_pair_aro_pol core_scoring_Score_100x_fa_pair_pol_pol core_scoring_Score_100x_h2o_hbond core_scoring_Score_100x_hbond_bb_sc core_scoring_Score_100x_hbond_lr_bb core_scoring_Score_100x_hbond_lr_bb_sc core_scoring_Score_100x_hbond_sc core_scoring_Score_100x_hbond_sr_bb core_scoring_Score_100x_hbond_sr_bb_sc core_scoring_Score_100x_pair core_scoring_Score_100x_rsigma core_scoring_Score_10x_fa_atr core_scoring_Score_10x_fa_rep core_scoring_Score_10x_fa_sol core_scoring_Score_10x_lk_costheta core_scoring_Score_10x_lk_nonpolar core_scoring_Score_10x_lk_polar core_scoring_Score_10x_occ_sol_fitted core_scoring_Score_1x_gb_elec core_scoring_Score_1x_pack_stat core_scoring_Score_1x_sa core_scoring_Score_200x_mm_bend core_scoring_Score_200x_mm_twist core_scoring_Score_40000x_p_aa core_scoring_Score_5000x_env core_scoring_Score_5x_occ_sol_fitted_onebody core_scoring_Score_analytic_etable_100x_fa_atr core_scoring_Score_analytic_etable_100x_fa_rep core_scoring_Score_analytic_etable_100x_fa_sol protocols_docking_DockingLowRes protocols_moves_ShearMover protocols_moves_SmallMover protocols_optimization_Minimizer_dfpmin_armijo protocols_optimization_Minimizer_dfpmin_armijo_nonmonotone protocols_relax_fast_relax_performance_benchmark_mmstd protocols_relax_fast_relax_performance_benchmark_sc12he protocols_relax_fast_relax_performance_benchmark_sc12sp2 utility_tag_Tag_Create
Test: linux.gcc.profile

Failed sub-tests (click for more details):
FloppyTail jd2test


branch: master 「№59590」
Commited by: Brandon Frenz
GitHub commit link: 「e4247166b964f2ea」
Difference from previous tested commit:  code diff
Commit date: 2017-07-14 14:25:12
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.addsan integration.mpi integration.release_debug integration.ubsan integration performance profile release.PyRosetta4.MinSizeRel linux.clang.score linux.gcc.score mac.clang.score

Merge pull request #2073 from RosettaCommons/bfrenz/FixDensScaling This code fixes the issue where the order in which you called protocols effected the density scoring values do the the initialize fast scoring first time function using the pose to setup the density scoring. Hopefully the effect is minor but density weights may need to change as a result. Especially if your protocol operated using a centroid model as input to rosetta.



branch: master 「№59589」
Commited by: Andrew Leaver-Fay
GitHub commit link: 「59a652f08f663811」
Difference from previous tested commit:  code diff
Commit date: 2017-07-14 08:27:19
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tutorials integration maintenance.documentation performance profile linux.clang.score linux.gcc.score mac.clang.score

Merge pull request #2384 from RosettaCommons/aleaverfay/jd3_multiple_results_per_job JD3: Jobs produce multiple of JobSummary/JobResult pairs Imagine that a job produces 1000 poses because it's efficient for it to produce many at once. What then? Should it put all 1000 poses into a single JobResult? When the JobQueen selects Pose 884 to advance to the next round of the protocol, will all 1000 Poses be sent as a single serialized JobResult to the remote node, so it can extract all 1000, and then take the single Pose it cares about? That seems like a bad idea! JD3's initial design didn't plan for this. The new system I'm working on here instead has a Job produce a list of outputs allowing the JobDistributor to serialize and store them all separately. Then when result 884 needs to get sent to the remote node as input to the next job, only a single Pose has to be transferred. Also, the other 999 poses can be deallocated. Job's ```run()``` method now returns a ```CompletedJobResult``` as before, but this previous typedef is now a struct containing a vector1 of JobSummary/JobResult pairs in addition to a JobStatus. If a job produces more than one Pose, each Pose could (should) be put into separate PoseJobResult and entered into a separate entry in the CompletedJobOutput array. The JobQueen's interface now changes: * ```note_job_completed(...)``` now informs the JQ of the number of job results produced * ```completed_job_summary( ... )``` now includes the index of the JobSummary (1..nresults for that job) * ```completed_job_result( ... )``` similarly includes the index of the JobResult * ```jobs_that_should_be_output``` now returns a list of Size/Size pairs * ```job_results_that_should_be_discarded``` also returns a list of Size/Size pairs The PoseOutputters now handle extra outputs the same way that JD2 handles multiple Pose outputs for a single job -- i.e. the names given to the extra poses written as .pdbs or silent structures append an extra _0001, _0002 after the job_id; e.g. job 4311 run on PDB 1l2y.pdb which produces < 9999 output Poses would write to 1l2y_4311_0001.pdb, 1l2y_4311_0002.pdb, etc. There's really no reason for the integration test changes I'm seeing on the server, and I'm suspicious that it's just a hiccup related to Frank's merge of PR #2371 which fixed several bugs in symmetric minimization.

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/apps/public/darc/DARC.cc src/apps/public/pepspec/pepspec.cc src/apps/public/pepspec/pepspec_anchor_dock.cc src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc src/apps/public/weight_optimization/torsional_potential_corrections.cc src/core/conformation/UltraLightResidue.cc src/core/conformation/symmetry/SymmetryInfo.cc src/core/io/silent/RNA_SilentStruct.cc src/core/optimization/Minimizer.cc src/core/pack/rotamers/SingleNCAARotamerLibraryCreator.cc src/core/scoring/ResidualDipolarCoupling.cc src/core/scoring/constraints/BigBinConstraint.cc src/core/scoring/constraints/ConstraintIO.cc src/core/scoring/dna/base_geometry.cc src/core/scoring/dssp/StrandPairing.cc src/core/scoring/facts/FACTSPotential.cc src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc src/core/scoring/membrane/MPEnvEnergy.cc src/core/scoring/methods/GaussianOverlapEnergy.cc src/core/scoring/methods/MembraneEnvSmoothEnergy.cc src/core/scoring/methods/ResidualDipolarCouplingEnergy_Rohl.cc src/core/scoring/orbitals/OrbitalsScore.cc src/core/scoring/packing/PoseBalls.cc src/core/scoring/power_diagram/PowerDiagram.cc src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc src/core/select/residue_selector/GlycanPositionSelector.cc src/devel/denovo_protein_design/DesignRelaxMover.cc src/devel/splice/Splice.cc src/protocols/antibody/AntibodyInfo.cc src/protocols/antibody/ModelCDRH3.cc src/protocols/cartesian/md.cc src/protocols/comparative_modeling/LoopRelaxMover.cc src/protocols/cryst/refinable_lattice.cc src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc src/protocols/denovo_design/components/SheetDB.cc src/protocols/enzdes/EnzdesFlexBBProtocol.cc src/protocols/enzdes/SecondaryMatchProtocol.cc src/protocols/enzdes/enzdes_util.cc src/protocols/forge/remodel/RemodelAccumulator.cc src/protocols/frag_picker/scores/PhiPsiRmsd.cc src/protocols/frags/TorsionFragment.cc src/protocols/hybridization/FragmentBiasAssigner.cc src/protocols/hybridization/TMalign.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loophash/LoopHashLibrary.cc src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc src/protocols/loops/loops_main.cc src/protocols/make_rot_lib/MakeRotLib.cc src/protocols/make_rot_lib/MakeRotLibMover.cc src/protocols/membrane/OptimizeMembranePositionMover.cc src/protocols/metal_interface/FindClosestAtom.cc src/protocols/moves/MoverStatus.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refinement.cc src/protocols/mpi_refinement/MultiObjective.cc src/protocols/mpi_refinement/util.cc src/protocols/noesy_assign/PeakFileFormat.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/pockets/Fingerprint.cc src/protocols/pockets/PocketGrid.cc src/protocols/rna/denovo/fragments/FullAtomRNA_Fragments.cc src/protocols/rna/movers/ErraserMinimizerMover.cc src/protocols/scoring/ImplicitFastClashCheck.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/sewing/sampling/MonteCarloAssemblyMover.cc src/protocols/simple_filters/ResidueIEFilter.cc src/protocols/simple_filters/SheetFilter.cc src/protocols/simple_moves/AddCavitiesMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/sparta/Sparta.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.cc src/protocols/stepwise/modeler/util.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/viewer/triangleIterator.cc src/utility/libsvm/Svm.cc test/core/conformation/UltraLightResidue.cxxtest.hh


branch: master 「№59588」
Commited by: Andrew Watkins
GitHub commit link: 「80f93bd0a1c30f6b」
Difference from previous tested commit:  code diff
Commit date: 2017-07-13 15:26:41
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python3.PyRosetta4.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration.tutorials integration maintenance.documentation performance profile release.PyRosetta4.Debug linux.clang.score linux.gcc.score mac.clang.score

Merge pull request #2393 from RosettaCommons/everyday847/stepwise_integration_test_pre_fix Pre-emptive alteration to 'stepwise' silent file tags (just in integration tests) The 14 integration test changes to stepwise integration tests are EXPECTED; they reflect a nomenclature change so it will be easier to detect REAL changes later.

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branch: master 「№59587」
Commited by: TJ Brunette
GitHub commit link: 「46dab53953a8e5c8」
Difference from previous tested commit:  code diff
Commit date: 2017-07-13 13:27:13
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score

Merge pull request #2388 from RosettaCommons/tjbrunette/near_native_fast_fix fix to closure_type flag in NearNativeLoopCloser

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branch: master 「№59586」
Commited by: Andrew Watkins
GitHub commit link: 「9ae4e0d3fa705e12」
Difference from previous tested commit:  code diff
Commit date: 2017-07-13 12:02:05
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score

Merge pull request #2391 from RosettaCommons/everyday847/my_app A fragment assembly UI app

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Test: mac.clang.integration

Failed sub-tests (click for more details):
autoNOE_rosetta


branch: master 「№59585」
Commited by: Jared Adolf-Bryfogle
GitHub commit link: 「c6d0f5696c3ef819」
Difference from previous tested commit:  code diff
Commit date: 2017-07-12 13:00:31
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration maintenance.documentation performance profile linux.clang.python2.release.PyRosetta4.Debug mac.clang.python2.7.release.PyRosetta4.Debug mac.clang.python3.5.release.PyRosetta4.Debug ubuntu.clang.python3.release.PyRosetta4.Debug mac.clang.python2.7.release.PyRosetta4.Release mac.clang.python3.5.release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score unit.ubsan

Merge pull request #2387 from RosettaCommons/jadolfbr/code_template_namespaces Fix Code Template Namespacing This addresses #2386 - Add full pathing or typedefs to function variables to make the templates independent of final namespace as they should be.

...
Test: linux.gcc.code_quality.beautification

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/apps/public/darc/DARC.cc src/apps/public/pepspec/pepspec.cc src/apps/public/pepspec/pepspec_anchor_dock.cc src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc src/apps/public/weight_optimization/torsional_potential_corrections.cc src/core/conformation/UltraLightResidue.cc src/core/conformation/symmetry/SymmetryInfo.cc src/core/io/silent/RNA_SilentStruct.cc src/core/optimization/Minimizer.cc src/core/pack/rotamers/SingleNCAARotamerLibraryCreator.cc src/core/scoring/ResidualDipolarCoupling.cc src/core/scoring/constraints/BigBinConstraint.cc src/core/scoring/constraints/ConstraintIO.cc src/core/scoring/dna/base_geometry.cc src/core/scoring/dssp/StrandPairing.cc src/core/scoring/facts/FACTSPotential.cc src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc src/core/scoring/membrane/MPEnvEnergy.cc src/core/scoring/methods/GaussianOverlapEnergy.cc src/core/scoring/methods/MembraneEnvSmoothEnergy.cc src/core/scoring/methods/ResidualDipolarCouplingEnergy_Rohl.cc src/core/scoring/orbitals/OrbitalsScore.cc src/core/scoring/packing/PoseBalls.cc src/core/scoring/power_diagram/PowerDiagram.cc src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc src/core/select/residue_selector/GlycanPositionSelector.cc src/devel/denovo_protein_design/DesignRelaxMover.cc src/devel/splice/Splice.cc src/protocols/antibody/AntibodyInfo.cc src/protocols/antibody/ModelCDRH3.cc src/protocols/cartesian/md.cc src/protocols/comparative_modeling/LoopRelaxMover.cc src/protocols/cryst/refinable_lattice.cc src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc src/protocols/denovo_design/components/SheetDB.cc src/protocols/enzdes/EnzdesFlexBBProtocol.cc src/protocols/enzdes/SecondaryMatchProtocol.cc src/protocols/enzdes/enzdes_util.cc src/protocols/forge/remodel/RemodelAccumulator.cc src/protocols/frag_picker/scores/PhiPsiRmsd.cc src/protocols/frags/TorsionFragment.cc src/protocols/hybridization/FragmentBiasAssigner.cc src/protocols/hybridization/TMalign.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loophash/LoopHashLibrary.cc src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc src/protocols/loops/loops_main.cc src/protocols/make_rot_lib/MakeRotLib.cc src/protocols/make_rot_lib/MakeRotLibMover.cc src/protocols/membrane/OptimizeMembranePositionMover.cc src/protocols/metal_interface/FindClosestAtom.cc src/protocols/moves/MoverStatus.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refinement.cc src/protocols/mpi_refinement/MultiObjective.cc src/protocols/mpi_refinement/util.cc src/protocols/noesy_assign/PeakFileFormat.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/pockets/Fingerprint.cc src/protocols/pockets/PocketGrid.cc src/protocols/rna/denovo/fragments/FullAtomRNA_Fragments.cc src/protocols/rna/movers/ErraserMinimizerMover.cc src/protocols/scoring/ImplicitFastClashCheck.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/sewing/sampling/MonteCarloAssemblyMover.cc src/protocols/simple_filters/ResidueIEFilter.cc src/protocols/simple_filters/SheetFilter.cc src/protocols/simple_moves/AddCavitiesMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/sparta/Sparta.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.cc src/protocols/stepwise/modeler/util.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/viewer/triangleIterator.cc src/utility/libsvm/Svm.cc test/core/conformation/UltraLightResidue.cxxtest.hh
Test: mac.clang.integration

Failed sub-tests (click for more details):
autoNOE_rosetta code_template_tests_src
Test: linux.gcc.performance

Failed sub-tests (click for more details):
core_import_pose_pose_from_pdbstring core_pack_denseig_score12 core_pack_linmem_ig_mmstd core_pack_linmem_ig_sc12he core_pack_linmem_ig_sc12sp2 core_pack_linmem_ig_score12 core_scoring_Score_10000x_cbeta core_scoring_Score_10000x_cbeta_smooth core_scoring_Score_10000x_cen_env_smooth core_scoring_Score_10000x_dslf_fa13 core_scoring_Score_10000x_omega core_scoring_Score_10000x_rama core_scoring_Score_10000x_rama2b core_scoring_Score_1000x_dslf_cbs_ds core_scoring_Score_1000x_fa_intra_rep core_scoring_Score_1000x_fa_intra_sol core_scoring_Score_1000x_p_aa_pp core_scoring_Score_100x_cart_bonded core_scoring_Score_100x_cen_pair_smooth core_scoring_Score_100x_cenpack_smooth core_scoring_Score_100x_ch_bond core_scoring_Score_100x_envsmooth core_scoring_Score_100x_fa_cust_pair_dist core_scoring_Score_100x_fa_dun core_scoring_Score_100x_fa_dun_dev core_scoring_Score_100x_fa_dun_rot core_scoring_Score_100x_fa_dun_semi core_scoring_Score_100x_h2o_hbond core_scoring_Score_100x_hbond_bb_sc core_scoring_Score_100x_hbond_lr_bb core_scoring_Score_100x_hbond_lr_bb_sc core_scoring_Score_100x_hbond_sc core_scoring_Score_100x_hbond_sr_bb core_scoring_Score_100x_hbond_sr_bb_sc core_scoring_Score_100x_ref_nc core_scoring_Score_10x_fa_atr core_scoring_Score_10x_fa_elec core_scoring_Score_10x_fa_rep core_scoring_Score_10x_fa_sol core_scoring_Score_10x_gauss core_scoring_Score_10x_lk_costheta core_scoring_Score_10x_lk_nonpolar core_scoring_Score_10x_lk_polar core_scoring_Score_10x_occ_sol_fitted core_scoring_Score_1x_gb_elec core_scoring_Score_1x_pack_stat core_scoring_Score_1x_sa core_scoring_Score_200x_mm_bend core_scoring_Score_200x_mm_twist core_scoring_Score_5000x_env core_scoring_Score_5x_occ_sol_fitted_onebody core_scoring_Score_analytic_etable_100x_fa_atr core_scoring_Score_analytic_etable_100x_fa_intra_rep core_scoring_Score_analytic_etable_100x_fa_rep core_scoring_Score_analytic_etable_100x_fa_sol protocols_docking_DockingLowRes protocols_ligand_docking_LigandDockProtocol protocols_moves_ShearMover protocols_moves_SmallMover protocols_optimization_Minimizer_dfpmin protocols_optimization_Minimizer_dfpmin_armijo protocols_optimization_Minimizer_dfpmin_armijo_nonmonotone protocols_relax_fast_relax_performance_benchmark_mmstd protocols_relax_fast_relax_performance_benchmark_sc12he protocols_relax_fast_relax_performance_benchmark_sc12sp2 protocols_relax_fast_relax_performance_benchmark_score12 utility_tag_Tag_Create
Test: linux.gcc.profile

Failed sub-tests (click for more details):
jd2test


branch: master 「№59584」
Commited by: Frank DiMaio
GitHub commit link: 「2e801d80f3974c79」
Difference from previous tested commit:  code diff
Commit date: 2017-07-10 13:13:20
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python3.PyRosetta4.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification code_quality.clang_analysis serialization integration.addsan integration.mpi integration.release_debug integration.tutorials integration.ubsan integration maintenance.documentation performance profile linux.clang.python2.release.PyRosetta4.Debug linux.clang.python3.release.PyRosetta4.Debug mac.clang.python2.7.release.PyRosetta4.Debug mac.clang.python3.5.release.PyRosetta4.Debug ubuntu.clang.python2.release.PyRosetta4.Debug linux.clang.python2.release.PyRosetta4.MinSizeRel linux.clang.python3.release.PyRosetta4.MinSizeRel mac.clang.python2.7.release.PyRosetta4.MinSizeRel mac.clang.python3.5.release.PyRosetta4.MinSizeRel ubuntu.clang.python2.release.PyRosetta4.MinSizeRel ubuntu.clang.python3.release.PyRosetta4.MinSizeRel linux.clang.python2.release.PyRosetta4.Release linux.clang.python3.release.PyRosetta4.Release mac.clang.python2.7.release.PyRosetta4.Release mac.clang.python3.5.release.PyRosetta4.Release ubuntu.clang.python2.release.PyRosetta4.Release ubuntu.clang.python3.release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score unit.addsan unit.valgrind

Merge pull request #2371 from RosettaCommons/aleaverfay/cart_min_deriv_unit_tests This checkin fixes two bugs with Cartesian minimization of symmetric poses. One was related to the recent change of symmetric atom tree minimizer to better support lattice symmetries. This change modified the edge weights on minimization graph, however CartesianMin still needed the old weights. This checkin changes the logic so the weights are modified as needed in SymAtomTree minimize, while keeping the minimization graph as it was before this change. This checkin also fixes a longstanding bug in symmetric CartesianMinimization when only part of the structure only was allowed to move. In these cases, the domain map was built assuming an asymmetric pose, leading to not all energy edges getting calculated during cartesian minimization. This has been fixed (and @aleaverfay has added an integration test ensuring this works). Thanks Andrew for finding these issues. Integration changes expected in all tests that minimize with symmetry.

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Test: linux.gcc.code_quality.beautification

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/apps/public/darc/DARC.cc src/apps/public/pepspec/pepspec.cc src/apps/public/pepspec/pepspec_anchor_dock.cc src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc src/apps/public/weight_optimization/torsional_potential_corrections.cc src/core/conformation/UltraLightResidue.cc src/core/conformation/symmetry/SymmetryInfo.cc src/core/io/silent/RNA_SilentStruct.cc src/core/optimization/Minimizer.cc src/core/pack/rotamers/SingleNCAARotamerLibraryCreator.cc src/core/scoring/ResidualDipolarCoupling.cc src/core/scoring/constraints/BigBinConstraint.cc src/core/scoring/constraints/ConstraintIO.cc src/core/scoring/dna/base_geometry.cc src/core/scoring/dssp/StrandPairing.cc src/core/scoring/facts/FACTSPotential.cc src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc src/core/scoring/membrane/MPEnvEnergy.cc src/core/scoring/methods/GaussianOverlapEnergy.cc src/core/scoring/methods/MembraneEnvSmoothEnergy.cc src/core/scoring/methods/ResidualDipolarCouplingEnergy_Rohl.cc src/core/scoring/orbitals/OrbitalsScore.cc src/core/scoring/packing/PoseBalls.cc src/core/scoring/power_diagram/PowerDiagram.cc src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc src/core/select/residue_selector/GlycanPositionSelector.cc src/devel/denovo_protein_design/DesignRelaxMover.cc src/devel/splice/Splice.cc src/protocols/antibody/AntibodyInfo.cc src/protocols/antibody/ModelCDRH3.cc src/protocols/cartesian/md.cc src/protocols/comparative_modeling/LoopRelaxMover.cc src/protocols/cryst/refinable_lattice.cc src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc src/protocols/denovo_design/components/SheetDB.cc src/protocols/enzdes/EnzdesFlexBBProtocol.cc src/protocols/enzdes/SecondaryMatchProtocol.cc src/protocols/enzdes/enzdes_util.cc src/protocols/forge/remodel/RemodelAccumulator.cc src/protocols/frag_picker/scores/PhiPsiRmsd.cc src/protocols/frags/TorsionFragment.cc src/protocols/hybridization/FragmentBiasAssigner.cc src/protocols/hybridization/TMalign.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loophash/LoopHashLibrary.cc src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc src/protocols/loops/loops_main.cc src/protocols/make_rot_lib/MakeRotLib.cc src/protocols/make_rot_lib/MakeRotLibMover.cc src/protocols/membrane/OptimizeMembranePositionMover.cc src/protocols/metal_interface/FindClosestAtom.cc src/protocols/moves/MoverStatus.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refinement.cc src/protocols/mpi_refinement/MultiObjective.cc src/protocols/mpi_refinement/util.cc src/protocols/noesy_assign/PeakFileFormat.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/pockets/Fingerprint.cc src/protocols/pockets/PocketGrid.cc src/protocols/rna/denovo/fragments/FullAtomRNA_Fragments.cc src/protocols/rna/movers/ErraserMinimizerMover.cc src/protocols/scoring/ImplicitFastClashCheck.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/sewing/sampling/MonteCarloAssemblyMover.cc src/protocols/simple_filters/ResidueIEFilter.cc src/protocols/simple_filters/SheetFilter.cc src/protocols/simple_moves/AddCavitiesMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/sparta/Sparta.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.cc src/protocols/stepwise/modeler/util.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/viewer/triangleIterator.cc src/utility/libsvm/Svm.cc test/core/conformation/UltraLightResidue.cxxtest.hh
Test: ubuntu.gcc.integration.addsan

Failed sub-tests (click for more details):
cluster_calibur farfar_mrna
Test: linux.gcc.mpi.serialization.integration.mpi

Failed sub-tests (click for more details):
threefold_symm_peptide_design
Test: linux.gcc.profile

Failed sub-tests (click for more details):
jd2test


branch: master 「№59583」
Commited by: Sergey Lyskov
GitHub commit link: 「e78c594d33dc5d23」
Difference from previous tested commit:  code diff
Commit date: 2017-07-09 16:00:34
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python3.PyRosetta4.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tutorials integration.valgrind integration maintenance.documentation performance profile mac.clang.python2.7.release.PyRosetta4.Debug mac.clang.python3.5.release.PyRosetta4.Debug mac.clang.python2.7.release.PyRosetta4.MinSizeRel mac.clang.python3.5.release.PyRosetta4.MinSizeRel linux.clang.python3.release.PyRosetta4.Release mac.clang.python2.7.release.PyRosetta4.Release mac.clang.python3.5.release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score unit.ubsan

Merge pull request #2385 from RosettaCommons/sergey/ui Updating UI project

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Test: linux.gcc.code_quality.beautification

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/apps/public/darc/DARC.cc src/apps/public/pepspec/pepspec.cc src/apps/public/pepspec/pepspec_anchor_dock.cc src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc src/apps/public/weight_optimization/torsional_potential_corrections.cc src/core/conformation/UltraLightResidue.cc src/core/conformation/symmetry/SymmetryInfo.cc src/core/io/silent/RNA_SilentStruct.cc src/core/optimization/Minimizer.cc src/core/pack/rotamers/SingleNCAARotamerLibraryCreator.cc src/core/scoring/ResidualDipolarCoupling.cc src/core/scoring/constraints/BigBinConstraint.cc src/core/scoring/constraints/ConstraintIO.cc src/core/scoring/dna/base_geometry.cc src/core/scoring/dssp/StrandPairing.cc src/core/scoring/facts/FACTSPotential.cc src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc src/core/scoring/membrane/MPEnvEnergy.cc src/core/scoring/methods/GaussianOverlapEnergy.cc src/core/scoring/methods/MembraneEnvSmoothEnergy.cc src/core/scoring/methods/ResidualDipolarCouplingEnergy_Rohl.cc src/core/scoring/orbitals/OrbitalsScore.cc src/core/scoring/packing/PoseBalls.cc src/core/scoring/power_diagram/PowerDiagram.cc src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc src/core/select/residue_selector/GlycanPositionSelector.cc src/devel/denovo_protein_design/DesignRelaxMover.cc src/devel/splice/Splice.cc src/protocols/antibody/AntibodyInfo.cc src/protocols/antibody/ModelCDRH3.cc src/protocols/cartesian/md.cc src/protocols/comparative_modeling/LoopRelaxMover.cc src/protocols/cryst/refinable_lattice.cc src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc src/protocols/denovo_design/components/SheetDB.cc src/protocols/enzdes/EnzdesFlexBBProtocol.cc src/protocols/enzdes/SecondaryMatchProtocol.cc src/protocols/enzdes/enzdes_util.cc src/protocols/forge/remodel/RemodelAccumulator.cc src/protocols/frag_picker/scores/PhiPsiRmsd.cc src/protocols/frags/TorsionFragment.cc src/protocols/hybridization/FragmentBiasAssigner.cc src/protocols/hybridization/TMalign.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loophash/LoopHashLibrary.cc src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc src/protocols/loops/loops_main.cc src/protocols/make_rot_lib/MakeRotLib.cc src/protocols/make_rot_lib/MakeRotLibMover.cc src/protocols/membrane/OptimizeMembranePositionMover.cc src/protocols/metal_interface/FindClosestAtom.cc src/protocols/moves/MoverStatus.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refinement.cc src/protocols/mpi_refinement/MultiObjective.cc src/protocols/mpi_refinement/util.cc src/protocols/noesy_assign/PeakFileFormat.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/pockets/Fingerprint.cc src/protocols/pockets/PocketGrid.cc src/protocols/rna/denovo/fragments/FullAtomRNA_Fragments.cc src/protocols/rna/movers/ErraserMinimizerMover.cc src/protocols/scoring/ImplicitFastClashCheck.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/sewing/sampling/MonteCarloAssemblyMover.cc src/protocols/simple_filters/ResidueIEFilter.cc src/protocols/simple_filters/SheetFilter.cc src/protocols/simple_moves/AddCavitiesMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/sparta/Sparta.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.cc src/protocols/stepwise/modeler/util.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/viewer/triangleIterator.cc src/utility/libsvm/Svm.cc test/core/conformation/UltraLightResidue.cxxtest.hh
Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
farfar_mrna


branch: master 「№59582」
Commited by: Labonte
GitHub commit link: 「4c640b3c8c3f8f04」
Difference from previous tested commit:  code diff
Commit date: 2017-07-08 20:37:20
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python3.PyRosetta4.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tutorials integration maintenance.documentation performance profile mac.clang.python2.7.release.PyRosetta4.Debug mac.clang.python3.5.release.PyRosetta4.Debug ubuntu.clang.python3.release.PyRosetta4.Debug linux.clang.python2.release.PyRosetta4.MinSizeRel linux.clang.python3.release.PyRosetta4.MinSizeRel mac.clang.python2.7.release.PyRosetta4.MinSizeRel mac.clang.python3.5.release.PyRosetta4.MinSizeRel release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score unit.valgrind

Merge pull request #2349 from RosettaCommons/JWLabonte/lipids/database This merge will add a few more lipid building blocks to the database for (an attempt at) explicit modeling of lipids. An integration test has also been added that demonstrates loading in an explicit lipid monolayer of 99 2-oleoyl-1-palmitoylphosphatidylcholine units, scoring, and minimizing. Please note that this integration test demonstrates a framework; it in no way implies any sort of scientific validity to the output structures. There is currently no reliable protocol for explicitly modeling lipid membranes in Rosetta. All unit tests pass. Several integration tests show new tracer output.

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Test: linux.gcc.code_quality.beautification

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/apps/public/darc/DARC.cc src/apps/public/pepspec/pepspec.cc src/apps/public/pepspec/pepspec_anchor_dock.cc src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc src/apps/public/weight_optimization/torsional_potential_corrections.cc src/core/conformation/UltraLightResidue.cc src/core/conformation/symmetry/SymmetryInfo.cc src/core/io/silent/RNA_SilentStruct.cc src/core/optimization/Minimizer.cc src/core/pack/rotamers/SingleNCAARotamerLibraryCreator.cc src/core/scoring/ResidualDipolarCoupling.cc src/core/scoring/constraints/BigBinConstraint.cc src/core/scoring/constraints/ConstraintIO.cc src/core/scoring/dna/base_geometry.cc src/core/scoring/dssp/StrandPairing.cc src/core/scoring/facts/FACTSPotential.cc src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc src/core/scoring/membrane/MPEnvEnergy.cc src/core/scoring/methods/GaussianOverlapEnergy.cc src/core/scoring/methods/MembraneEnvSmoothEnergy.cc src/core/scoring/methods/ResidualDipolarCouplingEnergy_Rohl.cc src/core/scoring/orbitals/OrbitalsScore.cc src/core/scoring/packing/PoseBalls.cc src/core/scoring/power_diagram/PowerDiagram.cc src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc src/core/select/residue_selector/GlycanPositionSelector.cc src/devel/denovo_protein_design/DesignRelaxMover.cc src/devel/splice/Splice.cc src/protocols/antibody/AntibodyInfo.cc src/protocols/antibody/ModelCDRH3.cc src/protocols/cartesian/md.cc src/protocols/comparative_modeling/LoopRelaxMover.cc src/protocols/cryst/refinable_lattice.cc src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc src/protocols/denovo_design/components/SheetDB.cc src/protocols/enzdes/EnzdesFlexBBProtocol.cc src/protocols/enzdes/SecondaryMatchProtocol.cc src/protocols/enzdes/enzdes_util.cc src/protocols/forge/remodel/RemodelAccumulator.cc src/protocols/frag_picker/scores/PhiPsiRmsd.cc src/protocols/frags/TorsionFragment.cc src/protocols/hybridization/FragmentBiasAssigner.cc src/protocols/hybridization/TMalign.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loophash/LoopHashLibrary.cc src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc src/protocols/loops/loops_main.cc src/protocols/make_rot_lib/MakeRotLib.cc src/protocols/make_rot_lib/MakeRotLibMover.cc src/protocols/membrane/OptimizeMembranePositionMover.cc src/protocols/metal_interface/FindClosestAtom.cc src/protocols/moves/MoverStatus.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refinement.cc src/protocols/mpi_refinement/MultiObjective.cc src/protocols/mpi_refinement/util.cc src/protocols/noesy_assign/PeakFileFormat.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/pockets/Fingerprint.cc src/protocols/pockets/PocketGrid.cc src/protocols/rna/denovo/fragments/FullAtomRNA_Fragments.cc src/protocols/rna/movers/ErraserMinimizerMover.cc src/protocols/scoring/ImplicitFastClashCheck.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/sewing/sampling/MonteCarloAssemblyMover.cc src/protocols/simple_filters/ResidueIEFilter.cc src/protocols/simple_filters/SheetFilter.cc src/protocols/simple_moves/AddCavitiesMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/sparta/Sparta.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.cc src/protocols/stepwise/modeler/util.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/viewer/triangleIterator.cc src/utility/libsvm/Svm.cc test/core/conformation/UltraLightResidue.cxxtest.hh
Test: linux.gcc.profile

Failed sub-tests (click for more details):
FloppyTail


branch: master 「№59581」
Commited by: Labonte
GitHub commit link: 「946605bf6d7697b5」
Difference from previous tested commit:  code diff
Commit date: 2017-07-06 19:36:36
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python3.PyRosetta4.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tutorials integration.ubsan integration maintenance.documentation performance profile linux.clang.python2.release.PyRosetta4.Debug linux.clang.python3.release.PyRosetta4.Debug mac.clang.python2.7.release.PyRosetta4.Debug mac.clang.python3.5.release.PyRosetta4.Debug linux.clang.python2.release.PyRosetta4.MinSizeRel linux.clang.python3.release.PyRosetta4.MinSizeRel mac.clang.python2.7.release.PyRosetta4.MinSizeRel mac.clang.python3.5.release.PyRosetta4.MinSizeRel linux.clang.python2.release.PyRosetta4.Release linux.clang.python3.release.PyRosetta4.Release mac.clang.python2.7.release.PyRosetta4.Release mac.clang.python3.5.release.PyRosetta4.Release ubuntu.clang.python2.release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score

Merge pull request #2382 from RosettaCommons/JWLabonte/sugars/database Carbohydrates: Another Xylose All tests pass. Expected integration change reporting +1 ResidueType.

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Test: linux.gcc.code_quality.beautification

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/apps/public/darc/DARC.cc src/apps/public/pepspec/pepspec.cc src/apps/public/pepspec/pepspec_anchor_dock.cc src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc src/apps/public/weight_optimization/torsional_potential_corrections.cc src/core/conformation/UltraLightResidue.cc src/core/conformation/symmetry/SymmetryInfo.cc src/core/io/silent/RNA_SilentStruct.cc src/core/optimization/Minimizer.cc src/core/pack/rotamers/SingleNCAARotamerLibraryCreator.cc src/core/scoring/ResidualDipolarCoupling.cc src/core/scoring/constraints/BigBinConstraint.cc src/core/scoring/constraints/ConstraintIO.cc src/core/scoring/dna/base_geometry.cc src/core/scoring/dssp/StrandPairing.cc src/core/scoring/facts/FACTSPotential.cc src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc src/core/scoring/membrane/MPEnvEnergy.cc src/core/scoring/methods/GaussianOverlapEnergy.cc src/core/scoring/methods/MembraneEnvSmoothEnergy.cc src/core/scoring/methods/ResidualDipolarCouplingEnergy_Rohl.cc src/core/scoring/orbitals/OrbitalsScore.cc src/core/scoring/packing/PoseBalls.cc src/core/scoring/power_diagram/PowerDiagram.cc src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc src/core/select/residue_selector/GlycanPositionSelector.cc src/devel/denovo_protein_design/DesignRelaxMover.cc src/devel/splice/Splice.cc src/protocols/antibody/AntibodyInfo.cc src/protocols/antibody/ModelCDRH3.cc src/protocols/cartesian/md.cc src/protocols/comparative_modeling/LoopRelaxMover.cc src/protocols/cryst/refinable_lattice.cc src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc src/protocols/denovo_design/components/SheetDB.cc src/protocols/enzdes/EnzdesFlexBBProtocol.cc src/protocols/enzdes/SecondaryMatchProtocol.cc src/protocols/enzdes/enzdes_util.cc src/protocols/forge/remodel/RemodelAccumulator.cc src/protocols/frag_picker/scores/PhiPsiRmsd.cc src/protocols/frags/TorsionFragment.cc src/protocols/hybridization/FragmentBiasAssigner.cc src/protocols/hybridization/TMalign.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loophash/LoopHashLibrary.cc src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc src/protocols/loops/loops_main.cc src/protocols/make_rot_lib/MakeRotLib.cc src/protocols/make_rot_lib/MakeRotLibMover.cc src/protocols/membrane/OptimizeMembranePositionMover.cc src/protocols/metal_interface/FindClosestAtom.cc src/protocols/moves/MoverStatus.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refinement.cc src/protocols/mpi_refinement/MultiObjective.cc src/protocols/mpi_refinement/util.cc src/protocols/noesy_assign/PeakFileFormat.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/pockets/Fingerprint.cc src/protocols/pockets/PocketGrid.cc src/protocols/rna/denovo/fragments/FullAtomRNA_Fragments.cc src/protocols/rna/movers/ErraserMinimizerMover.cc src/protocols/scoring/ImplicitFastClashCheck.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/sewing/sampling/MonteCarloAssemblyMover.cc src/protocols/simple_filters/ResidueIEFilter.cc src/protocols/simple_filters/SheetFilter.cc src/protocols/simple_moves/AddCavitiesMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/sparta/Sparta.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.cc src/protocols/stepwise/modeler/util.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/viewer/triangleIterator.cc src/utility/libsvm/Svm.cc test/core/conformation/UltraLightResidue.cxxtest.hh
Test: mac.clang.integration

Failed sub-tests (click for more details):
c-term_conjugation
Test: linux.gcc.performance

Failed sub-tests (click for more details):
core_import_pose_pose_from_pdbstring core_pack_denseig_score12 core_pack_linmem_ig_mmstd core_pack_linmem_ig_sc12he core_pack_linmem_ig_sc12sp2 core_pack_linmem_ig_score12 core_scoring_Score_10000x_cbeta core_scoring_Score_10000x_dslf_fa13 core_scoring_Score_10000x_omega core_scoring_Score_10000x_rama core_scoring_Score_10000x_rama2b core_scoring_Score_10000x_yhh_planarity core_scoring_Score_1000x_dslf_cbs_ds core_scoring_Score_1000x_mm_stretch core_scoring_Score_1000x_p_aa_pp core_scoring_Score_1000x_pro_close core_scoring_Score_100x_cart_bonded core_scoring_Score_100x_cen_pair_smooth core_scoring_Score_100x_cenpack_smooth core_scoring_Score_100x_ch_bond core_scoring_Score_100x_co core_scoring_Score_100x_envsmooth core_scoring_Score_100x_fa_cust_pair_dist core_scoring_Score_100x_fa_dun core_scoring_Score_100x_fa_dun_dev core_scoring_Score_100x_fa_dun_rot core_scoring_Score_100x_fa_dun_semi core_scoring_Score_100x_fa_pair core_scoring_Score_100x_fa_pair_aro_aro core_scoring_Score_100x_fa_pair_aro_pol core_scoring_Score_100x_fa_pair_pol_pol core_scoring_Score_100x_h2o_hbond core_scoring_Score_100x_hbond_bb_sc core_scoring_Score_100x_hbond_lr_bb core_scoring_Score_100x_hbond_lr_bb_sc core_scoring_Score_100x_hbond_sr_bb core_scoring_Score_100x_hbond_sr_bb_sc core_scoring_Score_100x_neigh_vect core_scoring_Score_100x_pair core_scoring_Score_100x_vdw core_scoring_Score_10x_fa_atr core_scoring_Score_10x_fa_elec core_scoring_Score_10x_fa_rep core_scoring_Score_10x_fa_sol core_scoring_Score_10x_gauss core_scoring_Score_10x_lk_costheta core_scoring_Score_10x_lk_nonpolar core_scoring_Score_10x_lk_polar core_scoring_Score_10x_occ_sol_fitted core_scoring_Score_1x_gb_elec core_scoring_Score_1x_pack_stat core_scoring_Score_1x_sa core_scoring_Score_200x_mm_bend core_scoring_Score_200x_mm_twist core_scoring_Score_5000x_env core_scoring_Score_5x_occ_sol_fitted_onebody core_scoring_Score_analytic_etable_100x_fa_atr core_scoring_Score_analytic_etable_100x_fa_rep core_scoring_Score_analytic_etable_100x_fa_sol protocols_docking_DockingLowRes protocols_moves_ShearMover protocols_moves_SmallMover protocols_optimization_Minimizer_dfpmin_armijo protocols_optimization_Minimizer_dfpmin_armijo_nonmonotone protocols_relax_fast_relax_performance_benchmark_mmstd protocols_relax_fast_relax_performance_benchmark_sc12he protocols_relax_fast_relax_performance_benchmark_sc12sp2 protocols_relax_fast_relax_performance_benchmark_score12 utility_tag_Tag_Create
Test: linux.gcc.profile

Failed sub-tests (click for more details):
FloppyTail jd2test


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