Test: mac.clang.python38.PyRosetta.unit 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20564」
Test files: 「file-system-view」 「file-list-view」
Daemon: hikaru-2     Started at: 2024-10-11 14:14:05     Run time: 0:39:49      State: build failed


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... ...truncated... 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CMakeFiles/protocols_d.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/stepwise/screener/SugarInstantiator.cc.o [4256/6560] Building CXX object CMakeFiles/protocols_d.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/stepwise/screener/VDW_BinScreener.cc.o [4257/6560] Building CXX object CMakeFiles/protocols_d.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/stepwise/sampler/protein/util.cc.o [4258/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/FoldTreeHybridize.cc.o [4259/6560] Building CXX object CMakeFiles/protocols_d.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/stepwise/screener/PartitionContactScreener.cc.o [4260/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/surface_docking/SurfaceOrientMover.cc.o [4261/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/surface_docking/CentroidRelaxMover.cc.o [4262/6560] Building CXX object CMakeFiles/protocols_c.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/flexpep_docking/FlexPepDockingFlags.cc.o [4263/6560] Building CXX object CMakeFiles/protocols_c.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/flexpep_docking/FlexPepDockingPoseMetrics.cc.o [4264/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/symmetric_docking/SymDockBaseProtocol.cc.o [4265/6560] Building CXX object CMakeFiles/protocols_c.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/flexpep_docking/FlexPepDockingLowRes.cc.o [4266/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/surface_docking/SurfaceParameters.cc.o [4267/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/ResolutionSwitcher.cc.o [4268/6560] Building CXX object CMakeFiles/protocols_c.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/flexpep_docking/FlexPepDockingAbInitio.cc.o [4269/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_build/LoopBuildMover.cc.o [4270/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/symmetric_docking/SymFoldandDockMoveRbJumpMover.cc.o [4271/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/symmetric_docking/SymRestrictTaskForDocking.cc.o [4272/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/DomainAssembly.cc.o [4273/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/AbrelaxMover.cc.o [4274/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/surface_docking/SurfaceVectorLoader.cc.o [4275/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/hybridization/HybridizeProtocol.cc.o [4276/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/FragmentSampler.cc.o [4277/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/ClaimerMessage.cc.o [4278/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/surface_docking/FullatomRelaxMover.cc.o [4279/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/symmetric_docking/SymFoldandDockRbTrialMover.cc.o [4280/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rbsegment_relax/util.cc.o [4281/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/symmetric_docking/SymSidechainMinMover.cc.o [4282/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/ConstraintEvaluatorWrapper.cc.o [4283/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/CutBiasClaimer.cc.o [4284/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/surface_docking/SurfaceDockingProtocol.cc.o [4285/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/symmetric_docking/membrane/MPSymDockMover.cc.o [4286/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/ClassicAbinitio.cc.o [4287/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/symmetric_docking/SymFoldandDockSlideTrialMover.cc.o [4288/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/BasicJumpClaimer.cc.o [4289/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/ConstraintEvaluatorWrapperCreator.cc.o [4290/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/DensityScoringClaimer.cc.o [4291/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/symmetric_docking/SymDockingLowRes.cc.o [4292/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/PcsEnergyController.cc.o [4293/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/ConstraintClaimer.cc.o [4294/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/symmetric_docking/SymDockingHiRes.cc.o [4295/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController.cc.o [4296/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/LoopFragmentClaimer.cc.o [4297/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts1.cc.o [4298/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/CoordConstraintClaimer.cc.o [4299/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/DisulfJumpClaimer.cc.o [4300/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts2.cc.o [4301/6560] Building CXX object 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[4318/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/SymmetryClaimer.cc.o [4319/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/TemplateFragmentClaimer.cc.o [4320/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/StartStructClaimer.cc.o [4321/6560] Building CXX object CMakeFiles/protocols_c.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/flexpep_docking/FlexPepDockingProtocol.cc.o [4322/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/TopologyClaimerFactory.cc.o [4323/6560] Building CXX object 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CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/MotifHit.cc.o [4336/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/abinitio/IterativeBase.cc.o [4337/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_build/LoopMover_SlidingWindow.cc.o [4338/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/loop_grower/SheetSampler.cc.o [4339/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/TMHTopologySamplerClaimer.cc.o [4340/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/Motif.cc.o [4341/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/topology_broker/TopologyBroker.cc.o [4342/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/noesy_assign/CrossPeak.cc.o [4343/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/IRCollection.cc.o [4344/6560] Building CXX object CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc.o FAILED: CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.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/IdentifyLigandMotifs.cc.o -MF CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc.o.d -o CMakeFiles/protocols_b.6.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc:782:31: error: expected ';' in 'for' statement specifier for ( auto sig_res_pos = 1 : mandatory_residues_for_motifs ){ ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc:782:31: error: expected expression 2 errors generated. 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{}