Test: linux.clang.performance 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20524」
Test files: 「file-system-view」 「file-list-view」
Daemon: sokudo-2     Started at: 2024-09-25 12:29:12     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 In file included from src/protocols/motifs/LigandDiscoverySearch.cc:131: src/protocols/motifs/LigandDiscoverySearch.hh:266:34: error: no member named 'Pose' in namespace 'core'; did you mean 'pose'? bool score_minipose(const core::Pose::pose & minipose, core::Real & fa_rep, core::Real & fa_atr, core::Real & fa_atr_rep_score_before) ~~~~~~^~~~ pose src/core/pose/xyzStripeHashPose.hh:22:11: note: 'pose' declared here namespace pose { ^ In file included from src/protocols/motifs/LigandDiscoverySearch.cc:131: src/protocols/motifs/LigandDiscoverySearch.hh:266:40: error: no type named 'pose' in namespace 'core::pose'; did you mean 'Pose'? bool score_minipose(const core::Pose::pose & minipose, core::Real & fa_rep, core::Real & fa_atr, core::Real & fa_atr_rep_score_before) ~~~~~~~~~~~~^~~~ Pose src/core/pose/Pose.hh:162:7: note: 'Pose' declared here class Pose : public utility::VirtualBase, public utility::pointer::enable_shared_from_this< Pose > ^ In file included from src/protocols/motifs/LigandDiscoverySearch.cc:131: src/protocols/motifs/LigandDiscoverySearch.hh:266:136: error: expected ';' at end of declaration list bool score_minipose(const core::Pose::pose & minipose, core::Real & fa_rep, core::Real & fa_atr, core::Real & fa_atr_rep_score_before) ^ ; src/protocols/motifs/LigandDiscoverySearch.cc:231:2: error: use of undeclared identifier 'working_pose_' working_pose_ = pose_from_PDB; ^ src/protocols/motifs/LigandDiscoverySearch.cc:348:2: error: use of undeclared identifier 'working_pose_' working_pose_ = pose_from_PDB; ^ src/protocols/motifs/LigandDiscoverySearch.cc:356:2: error: use of undeclared identifier 'working_pose_' working_pose_ = pose_pointer_helper; ^ src/protocols/motifs/LigandDiscoverySearch.cc:362:9: error: use of undeclared identifier 'working_pose_' return working_pose_; ^ src/protocols/motifs/LigandDiscoverySearch.cc:475:2: error: use of undeclared identifier 'working_pose_' working_pose_->append_residue_by_jump(*ligresOP, 1); ^ src/protocols/motifs/LigandDiscoverySearch.cc:479:44: error: use of undeclared identifier 'working_pose_' for ( core::Size resi_pos = 1; resi_pos < working_pose_->size(); ++resi_pos ) { ^ src/protocols/motifs/LigandDiscoverySearch.cc:481:8: error: use of undeclared identifier 'working_pose_' if ( working_pose_->residue(resi_pos).has_variant_type(core::chemical::DISULFIDE) ) { ^ src/protocols/motifs/LigandDiscoverySearch.cc:487:8: error: use of undeclared identifier 'working_pose_' if ( working_pose_->residue(working_pose_->size()).nbr_atom_xyz().distance(working_pose_->residue(resi_pos).nbr_atom_xyz()) < (working_pose_->residue(working_pose_->size()).nbr_radius() + working_pose_->residue(resi_pos).nbr_radius()) ) { ^ src/protocols/motifs/LigandDiscoverySearch.cc:487:31: error: use of undeclared identifier 'working_pose_' if ( working_pose_->residue(working_pose_->size()).nbr_atom_xyz().distance(working_pose_->residue(resi_pos).nbr_atom_xyz()) < (working_pose_->residue(working_pose_->size()).nbr_radius() + working_pose_->residue(resi_pos).nbr_radius()) ) { ^ src/protocols/motifs/LigandDiscoverySearch.cc:487:78: error: use of undeclared identifier 'working_pose_' if ( working_pose_->residue(working_pose_->size()).nbr_atom_xyz().distance(working_pose_->residue(resi_pos).nbr_atom_xyz()) < (working_pose_->residue(working_pose_->size()).nbr_radius() + working_pose_->residue(resi_pos).nbr_radius()) ) { ^ src/protocols/motifs/LigandDiscoverySearch.cc:487:130: error: use of undeclared identifier 'working_pose_' if ( working_pose_->residue(working_pose_->size()).nbr_atom_xyz().distance(working_pose_->residue(resi_pos).nbr_atom_xyz()) < (working_pose_->residue(working_pose_->size()).nbr_radius() + working_pose_->residue(resi_pos).nbr_radius()) ) { ^ src/protocols/motifs/LigandDiscoverySearch.cc:487:153: error: use of undeclared identifier 'working_pose_' if ( working_pose_->residue(working_pose_->size()).nbr_atom_xyz().distance(working_pose_->residue(resi_pos).nbr_atom_xyz()) < (working_pose_->residue(working_pose_->size()).nbr_radius() + working_pose_->residue(resi_pos).nbr_radius()) ) { ^ src/protocols/motifs/LigandDiscoverySearch.cc:487:191: error: use of undeclared identifier 'working_pose_' if ( working_pose_->residue(working_pose_->size()).nbr_atom_xyz().distance(working_pose_->residue(resi_pos).nbr_atom_xyz()) < (working_pose_->residue(working_pose_->size()).nbr_radius() + working_pose_->residue(resi_pos).nbr_radius()) ) { ^ src/protocols/motifs/LigandDiscoverySearch.cc:489:37: error: use of undeclared identifier 'working_pose_' minipose->append_residue_by_jump(working_pose_->residue(resi_pos), 1); ^ src/protocols/motifs/LigandDiscoverySearch.cc:499:35: error: use of undeclared identifier 'working_pose_' minipose->append_residue_by_jump(working_pose_->residue(working_pose_->size()), 1); ^ src/protocols/motifs/LigandDiscoverySearch.cc:499:58: error: use of undeclared identifier 'working_pose_' minipose->append_residue_by_jump(working_pose_->residue(working_pose_->size()), 1); ^ 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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