Test №852981

Test: mac.clang.python38.PyRosetta.unit 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20673」
Test files: 「file-system-view」「file-list-view」
Daemon: hikaru-2 Started at: 2025-03-25 16:38:58 Run time: 0:11:02 State: build failed

Test Log

Building PyRosetta MinSizeRel... Command line: cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/python/PyRosetta && /Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python-3.8.clang/516cea9b52ba95a8749b598875677062/bin/python3.8 build.py -j24 --compiler clang --type MinSizeRel --python-include-dir=/Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python-3.8.clang/516cea9b52ba95a8749b598875677062/include/python3.8 --python-lib=/Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python-3.8.clang/516cea9b52ba95a8749b598875677062/lib Creating PyRosetta in "MinSizeRel" mode in: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel Getting main repository root... cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source && git rev-parse --show-toplevel /Volumes/scratch/b3.w/rosetta/commits/rosetta Updating Pybind11 Git submodule... cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/.. && git submodule update --init -- source/external/pybind11 Updating Binder Git submodule... cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/.. && git submodule update --init -- source/src/python/PyRosetta/binder LLVM:6.0.1 + Binder install is detected at /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/prefix/llvm-6.0.1/llvm-6.0.1.macOS-12.6-x86_64-i386-64bit.release, skipping LLVM installation and Binder building procedures... Updating compilation submodules, version, options and residue-type-enum files... cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source && ./update_submodules.sh PyRosetta bcl zeromq && ./version.py && ./update_options.sh && ./update_ResidueType_enum_files.sh Updating submodules needed for compilation. Running versioning script ... Done. (0.2 seconds) Number of option files updated: 0 Total 4707 options. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed Generating bindings... cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/ && /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/prefix/llvm-6.0.1/llvm-6.0.1.macOS-12.6-x86_64-i386-64bit.release/bin/binder --config ./rosetta.config --root-module rosetta --prefix /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/all_rosetta_includes.hh -- -std=c++11 -isystem external -isystem external/include -isystem external/boost_submod -isystem external/dbio -isystem external/dbio/sqlite3 -isystem external/libxml2/include -isystem external/rdkit -isystem external/bcl/include -Isrc -Isrc/platform/macos -isysroot `xcrun --show-sdk-path` -DPYROSETTA -DNOCRASHREPORT -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DUNUSUAL_ALLOCATOR_DECLARATION -DNDEBUG -DBCL_NO_OS_SIGNAL_HANDLING -DPYROSETTA_BINDER Process input file /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/all_rosetta_includes.hh Generate bindings, pass 1... Generate bindings, pass 2... Generate bindings, pass 3... Generate bindings, pass 4... Generate bindings, pass 5... Generate bindings, pass 6... Generate bindings, pass 7... Sorting Binders... Sorting Binders... Done. Writing code... Writing code... Done. Writing /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/CMakeLists.txt Running CMake... cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/build/ && cmake -G Ninja -DCMAKE_BUILD_TYPE=MinSizeRel -DPYROSETTA_STRIP_MODULE=TRUE -DPYROSETTA_PYTHON_VERSION=3.8 -DPYTHON_LIBRARY=/Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python-3.8.clang/516cea9b52ba95a8749b598875677062/lib -DPYTHON_INCLUDE_DIR=/Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python-3.8.clang/516cea9b52ba95a8749b598875677062/include/python3.8 ../source -- Configuring done -- Generating done -- Build files have been written to: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/build Building... cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/build/ && ninja -j24 [1/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/TMscore.cc.o [2/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/UnfoldedStatePotential.cc.o [3/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/SASAPotential.cc.o [4/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/ResidueNeighborList.cc.o [5/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/SS_Info.cc.o [6/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/SplitUnfoldedTwoBodyPotential.cc.o [7/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/MinimizationGraph.cc.o [8/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/RamaPrePro.cc.o [9/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/OmegaTether.cc.o [10/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/PairEPotential.cc.o [11/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/PolymerBondedEnergyContainer.cc.o [12/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/ProQPotential.cc.o [13/5402] Building CXX 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object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/DomainAssembly.cc.o [2199/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/AbrelaxMover.cc.o [2200/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/FragmentSampler.cc.o [2201/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/Template.cc.o [2202/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/abscript/FragmentCM.cc.o [2203/5402] Building CXX object CMakeFiles/protocols_h.5.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/ligand_docking/GALigandDock/GALigandDock.cc.o [2204/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/constraint_generator/AutomaticSheetConstraintGenerator.cc.o [2205/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/abscript/AbscriptLoopCloserCM.cc.o [2206/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/ddg/ddG_main.cc.o [2207/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/ClassicAbinitio.cc.o [2208/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/vs_test.cc.o [2209/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/filters/ScorePoseSegmentFromResidueSelectorFilter.cc.o [2210/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/AlignByResidueSelectorMover.cc.o [2211/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/ResidueLabelsToPymolSelectionMover.cc.o [2212/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/LabelPoseFromResidueSelectorMover.cc.o [2213/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/abscript/RigidChunkCM.cc.o [2214/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/filters/RmsdFromResidueSelectorFilter.cc.o [2215/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/DisplayPoseLabelsMover.cc.o [2216/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/SavePDBInfoMover.cc.o [2217/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/selectors/CutpointResidueSelector.cc.o [2218/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/selectors/ProteinResidueSelector.cc.o [2219/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/ddg/ddGMover.cc.o [2220/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/NubInitioLoopClosureMover.cc.o [2221/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/DDomainParse.cc.o [2222/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/KinematicAbinitio.cc.o [2223/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/SplitAndMixPoseMover.cc.o [2224/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/ChunkTrialMover.cc.o [2225/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/MembraneAbinitio.cc.o [2226/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/utils/utils.cc.o [2227/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/ddg/CartesianddG.cc.o [2228/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/BackboneTorsionPerturbation.cc.o [2229/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/DomainAssembly.cc.o [2230/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/NubInitioMover.cc.o [2231/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/InsertChunkMover.cc.o [2232/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/FragmentBiasAssigner.cc.o [2233/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/utils/Nub.cc.o [2234/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/AbrelaxApplication.cc.o [2235/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/BackboneTorsionSampler.cc.o [2236/5402] Building CXX object CMakeFiles/protocols_c.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/flexpep_docking/FlexPepDockingProtocol.cc.o [2237/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/CartesianHybridize.cc.o [2238/5402] Building CXX object 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CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/JumpSetup.cc.o [2245/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/IterativeBase.cc.o [2246/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/BuildPosition.cc.o [2247/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_grower/util.cc.o [2248/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/util.cc.o [2249/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/ResiduePairJump.cc.o [2250/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/PairingLibrary.cc.o [2251/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/JumpSample.cc.o [2252/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_grower/SheetSampler.cc.o [2253/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/ResiduePairJumpSetup.cc.o [2254/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/MotifLibrary.cc.o [2255/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_build/LoopMover_SlidingWindow.cc.o [2256/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/CartesianSampler.cc.o [2257/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/util.cc.o [2258/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/MotifHit.cc.o [2259/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/SingleMotif.cc.o [2260/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/IRCollection.cc.o [2261/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/Motif.cc.o [2262/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/FoldTreeHybridize.cc.o [2263/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o FAILED: CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBCL_NO_OS_SIGNAL_HANDLING -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_SYSTEM_NO_DEPRECATED -DNDEBUG -DNOCRASHREPORT -DPTR_STD -DPYROSETTA -DUNUSUAL_ALLOCATOR_DECLARATION -I/Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python-3.8.clang/516cea9b52ba95a8749b598875677062/include/python3.8 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/src/platform/macos -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/libxml2/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/bcl/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/external/pybind11/include -std=c++14 -fvisibility=hidden -fvisibility-inlines-hidden -Os -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -fPIC -Werror=non-virtual-dtor -MD -MT CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o -MF CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o.d -o CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:544:81: error: expected ';' after expression utility::pointer::make_shared<core::scoring::constraints::CoordinateConstraint> sc_cst_set; ^ ; /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:544:82: error: use of undeclared identifier 'sc_cst_set' utility::pointer::make_shared<core::scoring::constraints::CoordinateConstraint> sc_cst_set; ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:547:2: error: use of undeclared identifier 'sc_cst_set' sc_cst_set->add_constraint( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_1, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_1 ), fx1 ) ); ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:550:2: error: use of undeclared identifier 'sc_cst_set' sc_cst_set->add_constraint( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_2, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_2 ), fx2 ) ); ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:553:2: error: use of undeclared identifier 'sc_cst_set' sc_cst_set->add_constraint( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_3, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_3 ), fx3 ) ); ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:555:32: error: use of undeclared identifier 'sc_cst_set' working_pose_->constraint_set(sc_cst_set); ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:544:2: warning: expression result unused [-Wunused-value] utility::pointer::make_shared<core::scoring::constraints::CoordinateConstraint> sc_cst_set; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning and 6 errors generated. [2264/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/noesy_assign/CrossPeak.cc.o [2265/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc.o [2266/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/noesy_assign/PeakAssignment.cc.o [2267/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/noesy_assign/ResonanceList.cc.o [2268/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/protein_mpnn/ProteinMPNNMover.cc.o [2269/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/protein_mpnn/ProteinMPNNProbabilitiesMetric.cc.o [2270/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/noesy_assign/CrossPeakList.cc.o [2271/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/noesy_assign/FragsToAtomDist.cc.o [2272/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/MotifDnaPacker.cc.o [2273/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/FragInsertAndAlignMover.cc.o [2274/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/AutoRBRelaxMover.cc.o [2275/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/IdealizeHelices.cc.o [2276/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_grower/FragmentExtension.cc.o [2277/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/RBSegmentRelax_main.cc.o [2278/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/HybridizeProtocol.cc.o [2279/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/RBSegmentMover.cc.o [2280/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/OptimizeThreading.cc.o [2281/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/motif_utils.cc.o [2282/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/MotifSearch.cc.o [2283/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandMotifSearch.cc.o [2284/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/RBSegmentRelax.cc.o [2285/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/ConfChangeMover.cc.o [2286/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_grower/LoopGrower.cc.o ninja: build stopped: subcommand failed. Encounter error while executing: cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/build/ && ninja -j24 Encounter error while executing: cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/build/ && ninja -j24 [1/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/TMscore.cc.o [2/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/UnfoldedStatePotential.cc.o [3/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/SASAPotential.cc.o [4/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/ResidueNeighborList.cc.o [5/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/SS_Info.cc.o [6/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/SplitUnfoldedTwoBodyPotential.cc.o [7/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/MinimizationGraph.cc.o [8/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/RamaPrePro.cc.o [9/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/OmegaTether.cc.o [10/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/PairEPotential.cc.o [11/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/PolymerBondedEnergyContainer.cc.o [12/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/ProQPotential.cc.o [13/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/NeighborList.cc.o [14/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/P_AA.cc.o [15/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/PointWaterPotential.cc.o [16/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/SmoothEnvPairPotential.cc.o [17/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/WaterAdductHBondPotential.cc.o [18/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/Ramachandran2B.cc.o [19/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/aa_composition_energy/AACompositionConstraint.cc.o [20/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/PoissonBoltzmannPotential.cc.o [21/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/ResidualDipolarCoupling.cc.o [22/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/atomic_depth/util.cc.o [23/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/VdWTinkerPotential.cc.o [24/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/carbohydrates/util.cc.o [25/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/aa_composition_energy/AACompositionEnergySetup.cc.o [26/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/SecondaryStructurePotential.cc.o [27/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/Ramachandran.cc.o [28/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/AmbiguousNMRConstraint.cc.o [29/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/carbon_hbonds/CarbonHBondPotential.cc.o [30/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/AtomPairConstraint.cc.o [31/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/bin_transitions/BinTransitionData.cc.o [32/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/MultipoleElecPotential.cc.o [33/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/AtomToAxisConstraint.cc.o [34/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/AngleConstraint.cc.o [35/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/atomic_depth/AtomicDepth.cc.o [36/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/carbon_hbonds/CarbonHBondEnergy.cc.o [37/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/bin_transitions/BinTransitionCalculator.cc.o [38/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/Constraints.cc.o [39/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/BackboneStubLinearConstraint.cc.o [40/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/BackboneStubConstraint.cc.o [41/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/dna/setup.cc.o [42/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/BasePairConstraint.cc.o [43/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/BigBinConstraint.cc.o [44/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/AmbiguousNMRDistanceConstraint.cc.o [45/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/BasicConstraintCreators.cc.o [46/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/CoordinateConstraint.cc.o [47/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/ConstraintsEnergy.cc.o [48/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/RTConstraint.cc.o [49/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/DihedralPairConstraint.cc.o [50/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/DistancePairConstraint.cc.o [51/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/DihedralConstraint.cc.o [52/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/NamedAtomPairConstraint.cc.o [53/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/NonResidueTypeConstraint.cc.o [54/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/LocalCoordinateConstraint.cc.o [55/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/MembraneSpanTermZConstraint.cc.o [56/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/NamedAngleConstraint.cc.o [57/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/MembraneSpanConstraint.cc.o [58/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/FabConstraint.cc.o [59/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/ConstraintIO.cc.o [60/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/NamedDihedralConstraint.cc.o [61/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/ResidueCouplingConstraint.cc.o [62/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/ResidueTypeConstraint.cc.o [63/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/ScoreFunction.cc.o [64/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/ResidueTypeLinkingConstraint.cc.o [65/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/SiteConstraintResidues.cc.o [66/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/ConstraintSet.cc.o [67/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/SiteConstraint.cc.o [68/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/disulfides/DisulfideMatchingDatabase.cc.o [69/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/cryst/util.cc.o [70/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/disulfides/DisulfideAtomIndices.cc.o [71/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/disulfides/DisulfideMatchingEnergyContainer.cc.o [72/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/disulfides/CentroidDisulfideEnergyContainer.cc.o [73/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/constraints/SequenceProfileConstraint.cc.o [74/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/dna/DNABFormPotential.cc.o [75/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/elec/electrie/ElecTrieEvaluator.cc.o [76/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/disulfides/FullatomDisulfideEnergyContainer.cc.o [77/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/dna/DNATorsionPotential.cc.o [78/5402] Building CXX object CMakeFiles/core.3.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/core/scoring/dna/DirectReadoutPotential.cc.o [79/5402] Building CXX object 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Building CXX object CMakeFiles/protocols_c.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/flexpep_docking/FlexPepDockingFlags.cc.o [2193/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/ResolutionSwitcher.cc.o [2194/5402] Building CXX object CMakeFiles/protocols_c.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/flexpep_docking/FlexPepDockingLowRes.cc.o [2195/5402] Building CXX object CMakeFiles/protocols_c.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/flexpep_docking/FlexPepDockingAbInitio.cc.o [2196/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_build/LoopBuildMover.cc.o [2197/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/TemplateJumpSetup.cc.o [2198/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/DomainAssembly.cc.o [2199/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/AbrelaxMover.cc.o [2200/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/FragmentSampler.cc.o [2201/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/Template.cc.o [2202/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/abscript/FragmentCM.cc.o [2203/5402] Building CXX object CMakeFiles/protocols_h.5.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/ligand_docking/GALigandDock/GALigandDock.cc.o [2204/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/constraint_generator/AutomaticSheetConstraintGenerator.cc.o [2205/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/abscript/AbscriptLoopCloserCM.cc.o [2206/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/ddg/ddG_main.cc.o [2207/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/ClassicAbinitio.cc.o [2208/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/vs_test.cc.o [2209/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/filters/ScorePoseSegmentFromResidueSelectorFilter.cc.o [2210/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/AlignByResidueSelectorMover.cc.o [2211/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/ResidueLabelsToPymolSelectionMover.cc.o [2212/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/LabelPoseFromResidueSelectorMover.cc.o [2213/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/abscript/RigidChunkCM.cc.o [2214/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/filters/RmsdFromResidueSelectorFilter.cc.o [2215/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/DisplayPoseLabelsMover.cc.o [2216/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/SavePDBInfoMover.cc.o [2217/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/selectors/CutpointResidueSelector.cc.o [2218/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/selectors/ProteinResidueSelector.cc.o [2219/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/ddg/ddGMover.cc.o [2220/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/NubInitioLoopClosureMover.cc.o [2221/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/DDomainParse.cc.o [2222/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/KinematicAbinitio.cc.o [2223/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/movers/SplitAndMixPoseMover.cc.o [2224/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/ChunkTrialMover.cc.o [2225/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/MembraneAbinitio.cc.o [2226/5402] Building CXX object 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CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/FragmentBiasAssigner.cc.o [2233/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/fold_from_loops/utils/Nub.cc.o [2234/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/AbrelaxApplication.cc.o [2235/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/BackboneTorsionSampler.cc.o [2236/5402] Building CXX object CMakeFiles/protocols_c.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/flexpep_docking/FlexPepDockingProtocol.cc.o [2237/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/CartesianHybridize.cc.o [2238/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/TMalign.cc.o [2239/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/HybridizeFoldtreeDynamic.cc.o [2240/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/DisulfPairingLibrary.cc.o [2241/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/MembraneJump.cc.o [2242/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_grower/DensSkeleton.cc.o [2243/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/MRMover.cc.o [2244/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/JumpSetup.cc.o [2245/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/IterativeBase.cc.o [2246/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/BuildPosition.cc.o [2247/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_grower/util.cc.o [2248/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/util.cc.o [2249/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/ResiduePairJump.cc.o [2250/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/PairingLibrary.cc.o [2251/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/JumpSample.cc.o [2252/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_grower/SheetSampler.cc.o [2253/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/ResiduePairJumpSetup.cc.o [2254/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/MotifLibrary.cc.o [2255/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_build/LoopMover_SlidingWindow.cc.o [2256/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/CartesianSampler.cc.o [2257/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/jumping/util.cc.o [2258/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/MotifHit.cc.o [2259/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/SingleMotif.cc.o [2260/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/IRCollection.cc.o [2261/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/Motif.cc.o [2262/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/FoldTreeHybridize.cc.o [2263/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o FAILED: CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBCL_NO_OS_SIGNAL_HANDLING -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_SYSTEM_NO_DEPRECATED -DNDEBUG -DNOCRASHREPORT -DPTR_STD -DPYROSETTA -DUNUSUAL_ALLOCATOR_DECLARATION -I/Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python-3.8.clang/516cea9b52ba95a8749b598875677062/include/python3.8 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/src/platform/macos -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/libxml2/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.8/minsizerel/source/external/bcl/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/external/pybind11/include -std=c++14 -fvisibility=hidden -fvisibility-inlines-hidden -Os -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -fPIC -Werror=non-virtual-dtor -MD -MT CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o -MF CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o.d -o CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:544:81: error: expected ';' after expression utility::pointer::make_shared<core::scoring::constraints::CoordinateConstraint> sc_cst_set; ^ ; /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:544:82: error: use of undeclared identifier 'sc_cst_set' utility::pointer::make_shared<core::scoring::constraints::CoordinateConstraint> sc_cst_set; ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:547:2: error: use of undeclared identifier 'sc_cst_set' sc_cst_set->add_constraint( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_1, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_1 ), fx1 ) ); ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:550:2: error: use of undeclared identifier 'sc_cst_set' sc_cst_set->add_constraint( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_2, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_2 ), fx2 ) ); ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:553:2: error: use of undeclared identifier 'sc_cst_set' sc_cst_set->add_constraint( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_3, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_3 ), fx3 ) ); ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:555:32: error: use of undeclared identifier 'sc_cst_set' working_pose_->constraint_set(sc_cst_set); ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:544:2: warning: expression result unused [-Wunused-value] utility::pointer::make_shared<core::scoring::constraints::CoordinateConstraint> sc_cst_set; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning and 6 errors generated. [2264/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/noesy_assign/CrossPeak.cc.o [2265/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc.o [2266/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/noesy_assign/PeakAssignment.cc.o [2267/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/noesy_assign/ResonanceList.cc.o [2268/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/protein_mpnn/ProteinMPNNMover.cc.o [2269/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/protein_mpnn/ProteinMPNNProbabilitiesMetric.cc.o [2270/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/noesy_assign/CrossPeakList.cc.o [2271/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/noesy_assign/FragsToAtomDist.cc.o [2272/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/MotifDnaPacker.cc.o [2273/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/FragInsertAndAlignMover.cc.o [2274/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/AutoRBRelaxMover.cc.o [2275/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/IdealizeHelices.cc.o [2276/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_grower/FragmentExtension.cc.o [2277/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/RBSegmentRelax_main.cc.o [2278/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/HybridizeProtocol.cc.o [2279/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/RBSegmentMover.cc.o [2280/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/OptimizeThreading.cc.o [2281/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/motif_utils.cc.o [2282/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/MotifSearch.cc.o [2283/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/LigandMotifSearch.cc.o [2284/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/RBSegmentRelax.cc.o [2285/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/ConfChangeMover.cc.o [2286/5402] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_grower/LoopGrower.cc.o ninja: build stopped: subcommand failed.

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