Test: linux.clang.build.debug 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20542」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-4     Started at: 2024-10-03 13:19:08     Run time: 0:01:25      State: failed


Running: /home/benchmark/prefix/nobu-4/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin cxx=clang extras= -j64 scons: Reading SConscript files ... Running versioning script ... Done. (0.1 seconds) Number of option files updated: 0 Total 4707 options. Updating submodules needed for compilation. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/motifs/LigandDiscoverySearch.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/motifs/LigandDiscoverySearch.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/anchored_design/AnchorMovers.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/anchored_design/AnchorMovers.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/anchored_design/AnchorMoversData.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/anchored_design/AnchorMoversData.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/DesignProteinBackboneAroundDNA.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DesignProteinBackboneAroundDNA.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/DnaChains.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DnaChains.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/DnaDesignDef.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DnaDesignDef.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/DnaInterfaceFinder.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DnaInterfaceFinder.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/DnaInterfaceMinMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DnaInterfaceMinMover.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/DnaInterfaceMultiStateDesign.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DnaInterfaceMultiStateDesign.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/DnaInterfacePacker.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DnaInterfacePacker.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/DNAParameters.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/DNAParameters.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/PDBOutput.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/PDBOutput.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/RestrictDesignToProteinDNAInterface.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/RestrictDesignToProteinDNAInterface.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/RotamerDNAHBondFilter.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/RotamerDNAHBondFilter.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/SeparateDnaFromNonDna.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/SeparateDnaFromNonDna.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/util.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/util.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/dna/WatsonCrickRotamerCouplings.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/dna/WatsonCrickRotamerCouplings.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/grafting/AnchoredGraftMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/grafting/AnchoredGraftMover.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/grafting/CCDEndsGraftMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 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-DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/grafting/GraftMoverBase.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/grafting/util.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/grafting/util.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/grafting/simple_movers/DeleteRegionMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/grafting/simple_movers/DeleteRegionMover.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/grafting/simple_movers/InsertPoseIntoPoseMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem 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build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/metal_interface/FindClosestAtom.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/metal_interface/FindClosestAtom.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/metal_interface/MatchGrafter.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ 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-Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/metal_interface/ZincHeterodimerMover.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/metal_interface/ZincSiteFinder.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/metal_interface/ZincSiteFinder.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/neighbor/Neighborhood.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/neighbor/Neighborhood.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/multistate_design/MetricCalculatorFitnessFunction.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ 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-Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pack_daemon/util.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/strong_types.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/strong_types.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/util.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/util.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/data_storage/DsspShiftArray.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/data_storage/DsspShiftArray.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/data_storage/PoseSegment.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/data_storage/PoseSegment.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/data_storage/PoseWithTerminalSegmentsOfKnownDSSP.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/data_storage/PoseWithTerminalSegmentsOfKnownDSSP.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/data_storage/SegmentEnvelope.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/data_storage/SegmentEnvelope.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/data_storage/TerminalDSSPSortedPoseVector.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/data_storage/TerminalDSSPSortedPoseVector.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/filters/CoreScorer.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/filters/CoreScorer.cc src/protocols/motifs/LigandDiscoverySearch.cc:740:66: error: non-const lvalue reference to type 'std::map<motif_atoms, protocols::motifs::MotifCOPs>' cannot bind to a value of unrelated type 'protocols::motifs::motif_atoms' (aka 'tuple<std::string, std::string, std::string, std::string, std::string, std::string, std::string>') protocols::motifs::hash_motif_library_into_map(motif_library_,mymap); ^~~~~ src/protocols/motifs/motif_utils.hh:281:134: note: passing argument to parameter 'mymap' here void hash_motif_library_into_map(protocols::motifs::MotifCOPs & input_library, std::map<motif_atoms, protocols::motifs::MotifCOPs> & mymap); ^ clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/filters/HasDisulfideFilter.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/filters/HasDisulfideFilter.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/movers/AddFlankingVirtualResiduesMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/movers/AddFlankingVirtualResiduesMover.cc src/protocols/motifs/LigandDiscoverySearch.cc:1432:20: error: no member named 'count' in 'std::tuple<std::basic_string<char>, std::basic_string<char>, std::basic_string<char>, std::basic_string<char>, std::basic_string<char>, std::basic_string<char>, std::basic_string<char> >' if ( mymap.count(curkey_tuple) > 0 ) { ~~~~~ ^ src/protocols/motifs/LigandDiscoverySearch.cc:1435:58: error: type 'protocols::motifs::motif_atoms' (aka 'tuple<std::string, std::string, std::string, std::string, std::string, std::string, std::string>') does not provide a subscript operator protocols::motifs::MotifCOPs real_motifs = mymap[curkey_tuple]; ~~~~~^~~~~~~~~~~~~ clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/movers/BlockwiseAnalysisMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/movers/BlockwiseAnalysisMover.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/movers/OmnibusDisulfideAnalysisLabelerMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/movers/OmnibusDisulfideAnalysisLabelerMover.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/movers/PickRandomSegmentMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/movers/PickRandomSegmentMover.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/movers/SewAnythingAddMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/movers/SewAnythingAddMover.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/simple_metrics/BlockwisePoseCompMotifMetric.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/simple_metrics/BlockwisePoseCompMotifMetric.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/simple_metrics/BlockwiseShapeCompMetric.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/simple_metrics/BlockwiseShapeCompMetric.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/simple_metrics/MinimumInterAlphaDistanceMetric.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/simple_metrics/MinimumInterAlphaDistanceMetric.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/pose_sewing/simple_metrics/WindowPoseCompMotifMetric.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pose_sewing/simple_metrics/WindowPoseCompMotifMetric.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/vip/VIP_Mover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/vip/VIP_Mover.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/vip/VIP_Report.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/vip/VIP_Report.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/vip/VIP_Utils.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/vip/VIP_Utils.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/movers/AssemblyMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/movers/AssemblyMover.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/movers/AppendAssemblyMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/movers/AppendAssemblyMover.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/movers/LigandBindingAssemblyMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ 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build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/scoring/MotifScorer.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/scoring/MotifScorer.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/scoring/TopNMotifScorer.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem 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-Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/scoring/SubsetPartnerMotifScorer.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/scoring/SegmentContactOrderScorer.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/scoring/SegmentContactOrderScorer.cc clang++ -o 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-DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/requirements/LigandAssemblyRequirement.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/requirements/AssemblyRequirementFactory.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/requirements/AssemblyRequirementFactory.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/requirements/ClashRequirement.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/requirements/ClashRequirement.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/requirements/KeepLigandContactsRequirement.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/requirements/KeepLigandContactsRequirement.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/requirements/LigandClashRequirement.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/requirements/LigandClashRequirement.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/requirements/DsspSpecificLengthRequirement.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/requirements/DsspSpecificLengthRequirement.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/requirements/LengthInResiduesRequirement.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/requirements/LengthInResiduesRequirement.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/requirements/SizeInSegmentsRequirement.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/requirements/SizeInSegmentsRequirement.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/requirements/NonTerminalStartingSegmentRequirement.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/requirements/NonTerminalStartingSegmentRequirement.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/hashing/ModelFileReader.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/hashing/ModelFileReader.cc clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/sewing/hashing/Hasher.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/hashing/Hasher.cc 3 errors generated. scons: *** [build/src/debug/linux/5.4/64/x86/clang/3.4/default/protocols/motifs/LigandDiscoverySearch.os] Error 1 scons: building terminated because of errors.
{}