Test: linux.clang.performance 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20518」
Test files: 「file-system-view」 「file-list-view」
Daemon: sokudo-2     Started at: 2024-09-24 17:08:43     Run time: 0:00:47      State: build failed


Test Log

Compiling: find bin -type l ! -name ".*" -exec rm {} \; ; /home/benchmark/prefix/sokudo-2/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin mode=release cxx=clang extras= -j4 scons: Reading SConscript files ... Running versioning script ... Done. (0.0 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/release/linux/5.4/64/x86/clang/3.4/default/protocols/peptide_deriver/PeptideDeriverMarkdownStreamOutputter.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/peptide_deriver/PeptideDeriverMarkdownStreamOutputter.cc 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 src/protocols/motifs/LigandDiscoverySearch.cc:988:6: error: use of undeclared identifier 'str'; did you mean 'std'? str::string pdb_name = ""; ^~~ std /bin/../lib/gcc/x86_64-redhat-linux/4.8.5/../../../../include/c++/4.8.5/bits/stl_queue.h:62:11: note: 'std' declared here namespace std _GLIBCXX_VISIBILITY(default) ^ src/protocols/motifs/LigandDiscoverySearch.cc:1309:71: error: use of undeclared identifier 'delta_score' std::tuple<core::Real, core::pose::Pose, std::string> pose_tuple(delta_score, *working_pose_, pdb_name); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1404:5: error: use of undeclared identifier 'clashing_counter' ++clashing_counter; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1416:5: error: use of undeclared identifier 'clashing_counter' ++clashing_counter; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1426:5: error: use of undeclared identifier 'clashing_counter' ++clashing_counter; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1430:4: error: use of undeclared identifier 'passed_placement_counter' ++passed_placement_counter; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1434:41: error: use of undeclared identifier 'ligresOP' working_pose_->append_residue_by_jump(*ligresOP, working_pose_->size(), "", "", true); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1440:174: error: use of undeclared identifier 'trip_atom_1' sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( 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 ) ) ); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1443:174: error: use of undeclared identifier 'trip_atom_2' sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( 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 ) ) ); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1446:174: error: use of undeclared identifier 'trip_atom_3' sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( 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 ) ) ); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1487:7: error: use of undeclared identifier 'ligand_added' if ( ligand_added == false ) { ^ src/protocols/motifs/LigandDiscoverySearch.cc:1488:3: error: use of undeclared identifier 'ligand_added' ligand_added = true; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1501:31: error: use of undeclared identifier 'lig_mrt'; did you mean 'lig_rt'? rts->add_base_residue_type(lig_mrt); ^~~~~~~ lig_rt src/protocols/motifs/LigandDiscoverySearch.cc:1498:34: note: 'lig_rt' declared here core::chemical::ResidueTypeCOP lig_rt(def_rts->name_mapOP(working_pose_->residue(working_pose_->size()).name())); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1501:9: error: no matching member function for call to 'add_base_residue_type' rts->add_base_residue_type(lig_mrt); ~~~~~^~~~~~~~~~~~~~~~~~~~~ src/core/chemical/PoseResidueTypeSet.hh:106:7: note: candidate function not viable: no known conversion from 'shared_ptr<const class core::chemical::ResidueType>' to 'shared_ptr<class core::chemical::MutableResidueType>' for 1st argument void add_base_residue_type( MutableResidueTypeOP new_type ) override; ^ src/core/chemical/PoseResidueTypeSet.hh:107:7: note: candidate function not viable: no known conversion from 'core::chemical::ResidueTypeCOP' (aka 'shared_ptr<const core::chemical::ResidueType>') to 'const std::string' (aka 'const basic_string<char>') for 1st argument void add_base_residue_type( std::string const & filename ) override; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1569:6: error: use of undeclared identifier 'clashing_counter' ++clashing_counter; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1588:6: error: use of undeclared identifier 'clashing_counter' ++clashing_counter; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1626:5: error: use of undeclared identifier 'clashing_counter' ++clashing_counter; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1638:13: error: use of undeclared identifier 'output_prefix' pdb_name = output_prefix + "_ResPos_" + std::to_string(working_position) + "_ResID_" + discovery_position_residue + "_Trio" + std::to_string(i) + "_" + ligresOP->name() + "_motif_" + motifcop->remark(); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1638:57: error: use of undeclared identifier 'working_position'; did you mean 'working_positions_'? pdb_name = output_prefix + "_ResPos_" + std::to_string(working_position) + "_ResID_" + discovery_position_residue + "_Trio" + std::to_string(i) + "_" + ligresOP->name() + "_motif_" + motifcop->remark(); ^~~~~~~~~~~~~~~~ working_positions_ src/protocols/motifs/LigandDiscoverySearch.hh:282:31: note: 'working_positions_' declared here utility::vector1<core::Size> working_positions_; ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. clang++ -o build/src/release/linux/5.4/64/x86/clang/3.4/default/protocols/jd2/AtomTreeDiffJobOutputter.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/jd2/AtomTreeDiffJobOutputter.cc clang++ -o build/src/release/linux/5.4/64/x86/clang/3.4/default/protocols/jd2/SerializedPoseJobInputter.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/jd2/SerializedPoseJobInputter.cc scons: *** [build/src/release/linux/5.4/64/x86/clang/3.4/default/protocols/motifs/LigandDiscoverySearch.os] Error 1 scons: building terminated because of errors.

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