Merge pull request #1733 from RosettaCommons/roccomoretti/clang_SA_fixes2
Some Clang Static Analysis Fixes
This hits most of them. The ones that are left are primarily "Value ... is never read" errors. Spot checking these, many (most?) look to be non-trivial. That is, the fact that the variable assignment is not read is pointing to a possible logic error in the code. These will likely need attention from subject-matter experts:
src/apps/public/darc/DARC.cc:125 Value stored to 'origin_space' during its initialization is never read
src/apps/public/pepspec/pepspec.cc:678 Value stored to 'ref_pep_end' is never read
src/apps/public/pepspec/pepspec.cc:680 Value stored to 'this_pep_end' is never read
src/apps/public/pepspec/pepspec.cc:745 Value stored to 'ref_pep_end' is never read
src/apps/public/pepspec/pepspec.cc:747 Value stored to 'this_pep_end' is never read
src/apps/public/pepspec/pepspec_anchor_dock.cc:359 Value stored to 'ref_pep_end' is never read
src/apps/public/pepspec/pepspec_anchor_dock.cc:361 Value stored to 'pep_end' is never read
src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc:316 Value stored to 'tx' is never read
src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc:317 Value stored to 'ty' is never read
src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc:318 Value stored to 'tz' is never read
src/apps/public/weight_optimization/torsional_potential_corrections.cc:1098 Value stored to 'dist2' is never read
src/apps/public/weight_optimization/torsional_potential_corrections.cc:1099 Value stored to 'dist2' is never read
src/core/conformation/symmetry/SymmetryInfo.cc:701 Value stored to 'fail' is never read
src/core/fragment/util.cc:598 Dereference of null pointer (loaded from variable 'left')
src/core/io/silent/RNA_SilentStruct.cc:344 Value stored to 'success' is never read
src/core/optimization/Minimizer.cc:517 Value stored to 'FAF' is never read
src/core/pack/rotamers/SingleNCAARotamerLibraryCreator.cc:150 Value stored to 'tried' is never read
src/core/scoring/ScoreFunction.cc:2311 Called C++ object pointer is null
src/core/scoring/ScoreFunction.cc:2318 Called C++ object pointer is null
src/core/scoring/constraints/BigBinConstraint.cc:189 Value stored to 'omega_lower_' is never read
src/core/scoring/constraints/BigBinConstraint.cc:190 Value stored to 'omega_upper_' is never read
src/core/scoring/constraints/ConstraintIO.cc:358 Value stored to 'start' is never read
src/core/scoring/dna/base_geometry.cc:677 Value stored to 'base_flipped' is never read
src/core/scoring/dna/base_geometry.cc:1122 Value stored to 'base_flipped' is never read
src/core/scoring/dssp/StrandPairing.cc:847 Value stored to 'reg' during its initialization is never read
src/core/scoring/facts/FACTSPotential.cc:726 Value stored to 'g2' is never read
src/core/scoring/hbonds/hbonds.cc:969 Value stored to 'frac2' is never read
src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc:466 Value stored to 'layer' is never read
src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc:468 Value stored to 'layer' is never read
src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc:549 Value stored to 'layer' is never read
src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc:551 Value stored to 'layer' is never read
src/core/scoring/membrane/MPEnvEnergy.cc:232 Value stored to 'layer' is never read
src/core/scoring/membrane/MPEnvEnergy.cc:234 Value stored to 'layer' is never read
src/core/scoring/membrane/MPEnvEnergy.cc:271 Value stored to 'layer' is never read
src/core/scoring/membrane/MPEnvEnergy.cc:272 Value stored to 'layer' is never read
src/core/scoring/methods/GaussianOverlapEnergy.cc:126 Value stored to 'score' is never read
src/core/scoring/methods/GaussianOverlapEnergy.cc:128 Value stored to 'score' is never read
src/core/scoring/methods/MembraneEnvSmoothEnergy.cc:444 Value stored to 'layer' is never read
src/core/scoring/methods/MembraneEnvSmoothEnergy.cc:446 Value stored to 'layer' is never read
src/core/scoring/methods/MembraneEnvSmoothEnergy.cc:522 Value stored to 'layer' is never read
src/core/scoring/methods/MembraneEnvSmoothEnergy.cc:524 Value stored to 'layer' is never read
src/core/scoring/methods/ResidualDipolarCouplingEnergy_Rohl.cc:316 Value stored to 'l' is never read
src/core/scoring/orbitals/OrbitalsScore.cc:418 Value stored to 'orb_orb_E' is never read
src/core/scoring/packing/PoseBalls.cc:295 Value stored to 'atype' is never read
src/core/scoring/packing/PoseBalls.cc:296 Value stored to 'atype' is never read
src/core/scoring/packing/PoseBalls.cc:297 Value stored to 'atype' is never read
src/core/scoring/packing/PoseBalls.cc:298 Value stored to 'atype' is never read
src/core/scoring/power_diagram/PowerDiagram.cc:1530 Value stored to 'arc_num_m1' is never read
src/core/scoring/power_diagram/PowerDiagram.cc:1532 Value stored to 'arc_num_p1' is never read
src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc:1578 Value stored to 'atmn' is never read
src/devel/denovo_protein_design/DesignRelaxMover.cc:114 Value stored to 'CurrentEnergy' during its initialization is never read
src/devel/splice/Splice.cc:657 Value stored to 'nearest_to_from' is never read
src/devel/splice/Splice.cc:658 Value stored to 'nearest_to_to' is never read
src/devel/splice/Splice.cc:1314 Value stored to 'tail_size' is never read
src/devel/splice/Splice.cc:1324 Value stored to 'tail_size' is never read
src/protocols/antibody/AntibodyInfo.cc:941 Value stored to 'is_H3' is never read
src/protocols/antibody/AntibodyInfo.cc:2114 Value stored to 'k' is never read
src/protocols/antibody/ModelCDRH3.cc:238 Value stored to 'unaligned_cdr_loop_end' is never read
src/protocols/cartesian/md.cc:1443 Value stored to 'start_score' is never read
src/protocols/comparative_modeling/LoopRelaxMover.cc:557 Value stored to 'current_sc' during its initialization is never read
src/protocols/comparative_modeling/LoopRelaxMover.cc:736 Value stored to 'current_sc' is never read
src/protocols/cryst/refinable_lattice.cc:355 Value stored to 'score' during its initialization is never read
src/protocols/denovo_design/components/SheetDB.cc:915 Value stored to 'prev_res' during its initialization is never read
src/protocols/enzdes/EnzdesFlexBBProtocol.cc:1865 Value stored to 'frag_unique' is never read
src/protocols/enzdes/SecondaryMatchProtocol.cc:683 Value stored to 'all_residues_compatible' is never read
src/protocols/enzdes/enzdes_util.cc:688 Value stored to 'found' is never read
src/protocols/farna/ErraserMinimizerMover.cc:734 Value stored to 'new_score' is never read
src/protocols/floppy_tail/FloppyTailMover.cc:561 Value stored to 'starttime' is never read
src/protocols/forge/remodel/RemodelAccumulator.cc:255 Value stored to 'boolReturn' is never read
src/protocols/frag_picker/scores/PhiPsiRmsd.cc:180 Value stored to 'stmp' is never read
src/protocols/frags/TorsionFragment.cc:836 Value stored to 'pose_nres' during its initialization is never read
src/protocols/hybridization/FragmentBiasAssigner.cc:623 Value stored to 'CCsum2' is never read
src/protocols/hybridization/TMalign.cc:505 Value stored to 'rms1' is never read
src/protocols/hybridization/TMalign.cc:1922 Value stored to 'seq_id' is never read
src/protocols/hybridization/TMalign.cc:2119 Value stored to 'TMmax' is never read
src/protocols/hybridization/TMalign.cc:2146 Value stored to 'TM' is never read
src/protocols/hybridization/TMalign.cc:2177 Value stored to 'simplify_step' is never read
src/protocols/hybridization/TMalign.cc:2178 Value stored to 'score_sum_method' is never read
src/protocols/loophash/LoopHashLibrary.cc:725 Value stored to 'stop_res' is never read
src/protocols/loophash/LoopHashLibrary.cc:726 Value stored to 'start_res' is never read
src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc:192 Value stored to 'local_debug' during its initialization is never read
src/protocols/loops/loops_main.cc:1399 Value stored to 'cutpoint' is never read
src/protocols/make_rot_lib/MakeRotLib.cc:206 Value stored to 'previous_ener' during its initialization is never read
src/protocols/make_rot_lib/MakeRotLibMover.cc:499 Value stored to 'previous_ener' during its initialization is never read
src/protocols/match/Matcher.cc:922 Value stored to 'failed_cast' is never read
src/protocols/match/Matcher.cc:928 Value stored to 'failed_cast' is never read
src/protocols/match/Matcher.cc:934 Value stored to 'failed_cast' is never read
src/protocols/match/Matcher.cc:940 Value stored to 'failed_cast' is never read
src/protocols/match/Matcher.cc:955 Value stored to 'failed_cast' is never read
src/protocols/match/Matcher.cc:961 Value stored to 'failed_cast' is never read
src/protocols/match/Matcher.cc:967 Value stored to 'failed_cast' is never read
src/protocols/match/Matcher.cc:973 Value stored to 'failed_cast' is never read
src/protocols/membrane/OptimizeMembranePositionMover.cc:269 Value stored to 'score_new' during its initialization is never read
src/protocols/membrane/OptimizeMembranePositionMover.cc:299 Value stored to 'score_old' is never read
src/protocols/membrane/OptimizeMembranePositionMover.cc:336 Value stored to 'score_new' during its initialization is never read
src/protocols/metal_interface/FindClosestAtom.cc:33 Value stored to 'temp_dis' during its initialization is never read
src/protocols/moves/MoverStatus.cc:33 Value stored to 'ms' is never read
src/protocols/mpi_refinement/Clusterer.cc:92 Value stored to 'dumm' is never read
src/protocols/mpi_refinement/Clusterer.cc:102 Value stored to 'dumm' is never read
src/protocols/mpi_refinement/MPI_Refinement.cc:380 Value stored to 'dumm' is never read
src/protocols/mpi_refinement/MultiObjective.cc:254 Value stored to 'dumm' is never read
src/protocols/mpi_refinement/MultiObjective.cc:260 Value stored to 'dumm' is never read
src/protocols/mpi_refinement/MultiObjective.cc:609 Value stored to 'dumm' is never read
src/protocols/mpi_refinement/MultiObjective.cc:615 Value stored to 'dumm' is never read
src/protocols/mpi_refinement/util.cc:619 Value stored to 'iatm_work' during its initialization is never read
src/protocols/noesy_assign/PeakFileFormat.cc:599 Value stored to 'weight' is never read
src/protocols/optimize_weights/IterativeOptEDriver.cc:4145 Value stored to 'no_tag_yet_assigned' is never read
src/protocols/pockets/Fingerprint.cc:106 Value stored to 'atom_serial_number' during its initialization is never read
src/protocols/pockets/Fingerprint.cc:113 Value stored to 'residue_sequence_number' during its initialization is never read
src/protocols/pockets/Fingerprint.cc:2136 Value stored to 'Differentiable_score' is never read
src/protocols/pockets/Fingerprint.cc:2158 Value stored to 'curr_angle1' during its initialization is never read
src/protocols/pockets/Fingerprint.cc:2159 Value stored to 'curr_angle2' during its initialization is never read
src/protocols/pockets/Fingerprint.cc:2160 Value stored to 'curr_angle3' during its initialization is never read
src/protocols/pockets/PocketGrid.cc:2217 Value stored to 'st' is never read
src/protocols/pockets/PocketGrid.cc:2225 Value stored to 'en' is never read
src/protocols/pockets/PocketGrid.cc:2241 Value stored to 'st' is never read
src/protocols/pockets/PocketGrid.cc:2249 Value stored to 'en' is never read
src/protocols/pockets/PocketGrid.cc:2265 Value stored to 'st' is never read
src/protocols/pockets/PocketGrid.cc:2273 Value stored to 'en' is never read
src/protocols/pockets/PocketGrid.cc:2667 Value stored to 'offset' is never read
src/protocols/pockets/PocketGrid.cc:2773 Value stored to 'offset' is never read
src/protocols/scoring/ImplicitFastClashCheck.cc:271 Value stored to 'bclash' is never read
src/protocols/seeded_abinitio/CoordinateCst.cc:262 Value stored to 'anchor_res' is never read
src/protocols/sewing/sampling/MonteCarloAssemblyMover.cc:117 Value stored to 'random_action' during its initialization is never read
src/protocols/simple_filters/ResidueIEFilter.cc:321 Value stored to 'whole_pose' during its initialization is never read
src/protocols/simple_filters/ResidueIEFilter.cc:322 Value stored to 'whole_interface' during its initialization is never read
src/protocols/simple_filters/SheetFilter.cc:1393 Value stored to 'stopp' is never read
src/protocols/simple_moves/AddCavitiesMover.cc:155 Value stored to 'Ncb' is never read
src/protocols/simple_moves/TailsScoreMover.cc:198 Value stored to 'updated_tail_score' during its initialization is never read
src/protocols/sparta/Sparta.cc:761 Value stored to 'pred_shift' is never read
src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.cc:1777 Value stored to 'range_end' is never read
src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc:1536 The right operand of '!=' is a garbage value
src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.cc:148 Value stored to 'jump_at_moving_suite' is never read
src/protocols/stepwise/modeler/util.cc:386 Value stored to 'found_root' is never read
src/protocols/toolbox/DecoySetEvaluation.cc:380 Value stored to 'invn' during its initialization is never read
src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc:131 Value stored to 'num_neighbors_' is never read
src/protocols/topology_broker/CoordConstraintClaimer.cc:123 Value stored to 'new_root' during its initialization is never read
src/protocols/topology_broker/TopologyBroker.cc:826 Value stored to 'ok' is never read
src/protocols/viewer/triangleIterator.cc:147 Value stored to 'starting' is never read