Test: linux.clang.profile 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20702」
Test files: 「file-system-view」 「file-list-view」
Daemon: sokudo-2     Started at: 2025-04-01 15:07:31     Run time: 0:01:33      State: build failed


Test Log

Building rosetta failed! 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 4710 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/protein_grid/ProteinGrid.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/protein_grid/ProteinGrid.cc src/protocols/protein_grid/ProteinGrid.cc:650:55: error: use of undeclared identifier 'res_num' core::Real atom_lj_radius = working_pose_->residue(res_num).atom_type(atom_num).lj_radius(); ^ src/protocols/protein_grid/ProteinGrid.cc:650:74: error: use of undeclared identifier 'atom_num' core::Real atom_lj_radius = working_pose_->residue(res_num).atom_type(atom_num).lj_radius(); ^ src/protocols/protein_grid/ProteinGrid.cc:865:11: error: no viable conversion from 'core::pose::PoseOP' (aka 'shared_ptr<core::pose::Pose>') to 'core::pose::Pose' return working_pose_; ^~~~~~~~~~~~~ src/core/pose/Pose.hh:210:2: note: candidate constructor not viable: no known conversion from 'core::pose::PoseOP' (aka 'shared_ptr<core::pose::Pose>') to 'const core::pose::Pose &' for 1st argument Pose( Pose const & src ); ^ src/protocols/protein_grid/ProteinGrid.cc:922:3: error: use of undeclared identifier 'pose'; did you mean 'core::pose'? pose::Pose matrix_pose; ^~~~ core::pose src/core/pose/Pose.hh:112:11: note: 'core::pose' declared here namespace pose { ^ src/protocols/protein_grid/ProteinGrid.cc:974:83: error: use of undeclared identifier 'fullness_ratio_' std::string matrix_pdb_name = pdb_name_prefix + "_WholeRatio_" + std::to_string(fullness_ratio_); ^ src/protocols/protein_grid/ProteinGrid.cc:977:6: error: use of undeclared identifier 'using_sub_area_' if(using_sub_area_) ^ src/protocols/protein_grid/ProteinGrid.cc:979:70: error: use of undeclared identifier 'sub_fullness_ratio_' matrix_pdb_name = matrix_pdb_name + "_SubRatio_" + std::to_string(sub_fullness_ratio_); ^ src/protocols/protein_grid/ProteinGrid.cc:988:3: error: use of undeclared identifier 'pose'; did you mean 'core::pose'? pose::Pose matrix_pose = export_protein_matrix_to_pose(); ^~~~ core::pose src/core/pose/Pose.hh:112:11: note: 'core::pose' declared here namespace pose { ^ src/protocols/protein_grid/ProteinGrid.cc:988:28: error: use of undeclared identifier 'export_protein_matrix_to_pose' pose::Pose matrix_pose = export_protein_matrix_to_pose(); ^ src/protocols/protein_grid/ProteinGrid.cc:994:15: error: no member named 'add_comment' in namespace 'core::pose' core::pose::add_comment(*working_pose_, "Corresponding space fill matrix file:", matrix_pdb_name); ~~~~~~~~~~~~^ src/protocols/protein_grid/ProteinGrid.cc:994:28: error: use of undeclared identifier 'working_pose_' core::pose::add_comment(*working_pose_, "Corresponding space fill matrix file:", matrix_pdb_name); ^ 11 errors generated. 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 clang++ -o build/src/release/linux/5.4/64/x86/clang/3.4/default/protocols/jd2/SerializedPoseJobOutputter.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/SerializedPoseJobOutputter.cc scons: *** [build/src/release/linux/5.4/64/x86/clang/3.4/default/protocols/protein_grid/ProteinGrid.os] Error 1 clang++ -o build/src/release/linux/5.4/64/x86/clang/3.4/default/protocols/jd2/archive/ArchiveManager.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/archive/ArchiveManager.cc scons: building terminated because of errors.

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