Test: linux.clang.build.release 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20707」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-1     Started at: 2025-04-02 16:14:17     Run time: 0:04:05      State: failed


Running: /home/benchmark/prefix/nobu-1/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin cxx=clang extras= mode=release -j48 scons: Reading SConscript files ... Running versioning script ... Done. (0.1 seconds) Number of option files updated: 0 Total 4709 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/release/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 -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -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 In file included from src/protocols/motifs/LigandDiscoverySearch.cc:131: src/protocols/motifs/LigandDiscoverySearch.hh:276:27: error: no type named 'ProteinGridOP' in namespace 'protocols::protein_grid'; did you mean 'ProteinGrid'? protocols::protein_grid::ProteinGridOP clash_pose_grid_; ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ ProteinGrid src/protocols/protein_grid/ProteinGrid.fwd.hh:20:7: note: 'ProteinGrid' declared here class ProteinGrid; // fwd declaration ^ In file included from src/protocols/motifs/LigandDiscoverySearch.cc:131: src/protocols/motifs/LigandDiscoverySearch.hh:276:41: error: field has incomplete type 'protocols::protein_grid::ProteinGrid' protocols::protein_grid::ProteinGridOP clash_pose_grid_; ^ src/protocols/protein_grid/ProteinGrid.fwd.hh:20:7: note: forward declaration of 'protocols::protein_grid::ProteinGrid' class ProteinGrid; // fwd declaration ^ In file included from src/protocols/motifs/LigandDiscoverySearch.cc:131: src/protocols/motifs/LigandDiscoverySearch.hh:281:27: error: no type named 'ProteinGridOP' in namespace 'protocols::protein_grid'; did you mean 'ProteinGrid'? protocols::protein_grid::ProteinGridOP sf_pose_grid_; ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ ProteinGrid src/protocols/protein_grid/ProteinGrid.fwd.hh:20:7: note: 'ProteinGrid' declared here class ProteinGrid; // fwd declaration ^ In file included from src/protocols/motifs/LigandDiscoverySearch.cc:131: src/protocols/motifs/LigandDiscoverySearch.hh:281:41: error: field has incomplete type 'protocols::protein_grid::ProteinGrid' protocols::protein_grid::ProteinGridOP sf_pose_grid_; ^ src/protocols/protein_grid/ProteinGrid.fwd.hh:20:7: note: forward declaration of 'protocols::protein_grid::ProteinGrid' class ProteinGrid; // fwd declaration ^ src/protocols/motifs/LigandDiscoverySearch.cc:231:24: error: exception specification in declaration does not match previous declaration LigandDiscoverySearch::~LigandDiscoverySearch() = default; ^ src/protocols/motifs/LigandDiscoverySearch.hh:116:2: note: previous declaration is here ~LigandDiscoverySearch(); ^ src/protocols/motifs/LigandDiscoverySearch.cc:772:27: error: no matching constructor for initialization of 'protocols::protein_grid::ProteinGrid' clash_pose_grid_(new protocols::protein_grid::ProteinGrid(working_pose_, resolution_increase_factor, binding_pocket_center_xyz, binding_pocket_dimensions)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/protocols/protein_grid/ProteinGrid.hh:62:2: note: candidate constructor not viable: no known conversion from 'utility::vector1<core::Size>' to 'numeric::xyzVector<int>' for 3rd argument ProteinGrid(core::pose::PoseOP in_pose, core::Real resolution, numeric::xyzVector<int> sub_area_center, utility::vector1<core::Size> sub_region_dimensions); ^ src/protocols/protein_grid/ProteinGrid.hh:53:2: note: candidate constructor not viable: requires single argument 'in_pose', but 4 arguments were provided ProteinGrid(core::pose::PoseOP in_pose); ^ src/protocols/protein_grid/ProteinGrid.hh:56:2: note: candidate constructor not viable: requires 2 arguments, but 4 were provided ProteinGrid(core::pose::PoseOP in_pose, core::Real resolution); ^ src/protocols/protein_grid/ProteinGrid.hh:59:2: note: candidate constructor not viable: requires 3 arguments, but 4 were provided ProteinGrid(core::pose::PoseOP in_pose, numeric::xyzVector<int> sub_area_center, utility::vector1<core::Size> sub_region_dimensions); ^ src/protocols/protein_grid/ProteinGrid.hh:65:2: note: candidate constructor not viable: requires single argument 'other', but 4 arguments were provided ProteinGrid( ProteinGrid const & other ); ^ src/protocols/protein_grid/ProteinGrid.hh:137:2: note: candidate constructor not viable: requires 0 arguments, but 4 were provided ProteinGrid(); ^ src/protocols/motifs/LigandDiscoverySearch.cc:775:4: error: expected expression else ^ src/protocols/motifs/LigandDiscoverySearch.cc:794:28: error: no member named 'ProteinGridOP' in namespace 'protocols::protein_grid'; did you mean 'ProteinGrid'? protocols::protein_grid::ProteinGridOP working_sf_pose_grid(new protocols::protein_grid::ProteinGrid(*sf_pose_grid_)); ~~~~~~~~~~~~~~~~~~~~~~~~~^ src/protocols/protein_grid/ProteinGrid.hh:43:7: note: 'ProteinGrid' declared here class ProteinGrid ^ src/protocols/motifs/LigandDiscoverySearch.cc:800:24: error: use of undeclared identifier 'working_sf_pose_grid' occupied_ratios[1] = working_sf_pose_grid->get_grid_occupied_cell_ratio(); ^ src/protocols/motifs/LigandDiscoverySearch.cc:801:24: error: use of undeclared identifier 'working_sf_pose_grid' occupied_ratios[2] = working_sf_pose_grid->get_sub_grid_occupied_cell_ratio(); ^ src/protocols/motifs/LigandDiscoverySearch.cc:958:7: error: use of undeclared identifier 'working_sf_pose_grid' working_sf_pose_grid->placed_ligand_space_fill_analysis(ligresOP); ^ src/protocols/motifs/LigandDiscoverySearch.cc:961:30: error: use of undeclared identifier 'working_sf_pose_grid' space_fill_scores[1] = working_sf_pose_grid->get_grid_occupied_cell_ratio(); ^ src/protocols/motifs/LigandDiscoverySearch.cc:962:30: error: use of undeclared identifier 'working_sf_pose_grid' space_fill_scores[2] = working_sf_pose_grid->get_sub_grid_occupied_cell_ratio(); ^ src/protocols/motifs/LigandDiscoverySearch.cc:979:8: error: use of undeclared identifier 'working_sf_pose_grid' working_sf_pose_grid->export_protein_matrix_to_pdb(matrix_pdb_prefix); ^ 14 errors generated. clang++ -o build/src/release/linux/5.4/64/x86/clang/3.4/default/libutility.so -stdlib=libstdc++ -shared -stdlib=libstdc++ -Wl,-rpath=/home/benchmark/rosetta/source/build/external/release/linux/5.4/64/x86/clang/3.4/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/backtrace.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/Binary_Util.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/crash_report.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/CSI_Sequence.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/curl.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/dating.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/exit.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/heap.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/inline_file_provider.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/integer_mapping.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/json_utilities.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/LexicographicalIterator.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/mpi_util.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/SimulateMPI.os 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build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/file/PathName.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/graph/ArrayPool.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/graph/DisjointSets.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/graph/Digraph.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/graph/Graph.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/graph/graph_util.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/graph/LowMemGraph.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/io/FileContentsMap.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/io/GeneralFileManager.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/io/icstream.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/io/izstream.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/io/ocstream.os 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build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/json_spirit/json_spirit_writer.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/json_spirit/json_spirit_tools.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/BooleanOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/BooleanVectorOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/FileOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/FileVectorOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/IntegerOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/IntegerVectorOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/Option.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/OptionCollection.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/PathOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/PathVectorOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/RealOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/RealVectorOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/ResidueChainVectorOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/ScalarOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/StringOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/StringVectorOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/VectorOption.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/mpi_stderr.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/OptionKeyList.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/OptionKeys.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/AnyOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/AnyVectorOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/BooleanOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/BooleanVectorOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/FileOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/FileVectorOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/IntegerOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/IntegerVectorOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/OptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/PathOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/PathVectorOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/RealOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/RealVectorOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/ResidueChainVectorOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/ScalarOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/StringOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/StringVectorOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/options/keys/VectorOptionKey.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/py/PyExitCallback.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/serialization/serialization.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/serialization/ObjexxFCL/DynamicIndexRange.srlz.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/serialization/ObjexxFCL/FArray1D.srlz.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/serialization/ObjexxFCL/FArray2D.srlz.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/serialization/ObjexxFCL/FArray3D.srlz.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/serialization/ObjexxFCL/ubyte.srlz.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/sql_database/DatabaseSessionManager.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/sql_database/types.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/tag/Tag.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/tag/util.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/tag/XMLSchemaGeneration.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/tag/XMLSchemaValidation.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/thread/ReadWriteMutex.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/xsd_util/util.os -Lexternal/lib -Lbuild/src/release/linux/5.4/64/x86/clang/3.4/default -Lsrc -Lbuild/external/release/linux/5.4/64/x86/clang/3.4/default -Lexternal -L/usr/lib -L/usr/local/lib -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes clang++ -o build/src/release/linux/5.4/64/x86/clang/3.4/default/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.o -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 -O3 -Wno-unused-variable -Wno-unused-parameter -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc scons: *** [build/src/release/linux/5.4/64/x86/clang/3.4/default/protocols/motifs/LigandDiscoverySearch.os] Error 1 In file included from src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc:126: src/protocols/motifs/LigandDiscoverySearch.hh:276:27: error: no type named 'ProteinGridOP' in namespace 'protocols::protein_grid'; did you mean 'ProteinGrid'? protocols::protein_grid::ProteinGridOP clash_pose_grid_; ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ ProteinGrid src/protocols/protein_grid/ProteinGrid.fwd.hh:20:7: note: 'ProteinGrid' declared here class ProteinGrid; // fwd declaration ^ In file included from src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc:126: src/protocols/motifs/LigandDiscoverySearch.hh:276:41: error: field has incomplete type 'protocols::protein_grid::ProteinGrid' protocols::protein_grid::ProteinGridOP clash_pose_grid_; ^ src/protocols/protein_grid/ProteinGrid.fwd.hh:20:7: note: forward declaration of 'protocols::protein_grid::ProteinGrid' class ProteinGrid; // fwd declaration ^ In file included from src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc:126: src/protocols/motifs/LigandDiscoverySearch.hh:281:27: error: no type named 'ProteinGridOP' in namespace 'protocols::protein_grid'; did you mean 'ProteinGrid'? protocols::protein_grid::ProteinGridOP sf_pose_grid_; ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ ProteinGrid src/protocols/protein_grid/ProteinGrid.fwd.hh:20:7: note: 'ProteinGrid' declared here class ProteinGrid; // fwd declaration ^ In file included from src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc:126: src/protocols/motifs/LigandDiscoverySearch.hh:281:41: error: field has incomplete type 'protocols::protein_grid::ProteinGrid' protocols::protein_grid::ProteinGridOP sf_pose_grid_; ^ src/protocols/protein_grid/ProteinGrid.fwd.hh:20:7: note: forward declaration of 'protocols::protein_grid::ProteinGrid' class ProteinGrid; // fwd declaration ^ 4 errors generated. scons: *** [build/src/release/linux/5.4/64/x86/clang/3.4/default/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.o] Error 1 scons: building terminated because of errors.
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