Test: linux.gcc.unit 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20516」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-1     Started at: 2024-09-24 17:01:33     Run time: 0:01:34      State: build failed


Compiling: find bin -type l ! -name ".*" -exec rm {} \; ; /home/benchmark/prefix/nobu-1/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin mode=debug cxx=gcc extras= -j48 && /home/benchmark/prefix/nobu-1/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py cxx=gcc mode=debug extras= cat=test -j48 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 ... g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/protocols/peptide_deriver/PeptideDeriverMarkdownStreamOutputter.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/peptide_deriver/PeptideDeriverMarkdownStreamOutputter.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/protocols/motifs/LigandDiscoverySearch.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/motifs/LigandDiscoverySearch.cc src/protocols/motifs/LigandDiscoverySearch.cc: In member function 'core::Size LigandDiscoverySearch::discover(std::string)': src/protocols/motifs/LigandDiscoverySearch.cc:987:52: error: 'score_placed_ligand' was not declared in this scope if(score_placed_ligand(minipose, original_pose)) ^ src/protocols/motifs/LigandDiscoverySearch.cc:1001:46: error: 'pdb_short_unique_name' was not declared in this scope ilm.process_for_motifs(*working_pose_, pdb_short_unique_name, placement_library, prot_pos_that_made_motifs_size); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1026:7: error: 'pdb_name' was not declared in this scope pdb_name = pdb_name + "_motifs_" + std::to_string(motifs_made); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1029:7: error: 'comment_table_data' was not declared in this scope comment_table_data = comment_table_data + std::to_string(motifs_made) + ","; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1259:7: error: 'comment_table_data' was not declared in this scope comment_table_data = comment_table_data + "," + "," + "," + ","; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1262:6: error: 'comment_table_header' was not declared in this scope comment_table_header = comment_table_header + "total_motif_count,significant_motif_count,real_motif_count,real_motif_ratio,"; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1265:6: error: 'pdb_name' was not declared in this scope pdb_name = pdb_name + ".pdb"; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1274:6: error: 'comment_table_data' was not declared in this scope comment_table_data = "," + pdb_name + "," + comment_table_data; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1303:71: error: 'delta_score' was not declared in this scope std::tuple<core::Real, core::pose::Pose, std::string> pose_tuple(delta_score, *working_pose_, pdb_name); ^ src/protocols/motifs/LigandDiscoverySearch.cc:799:9: error: unused variable 'ligand_added' [-Werror=unused-variable] bool ligand_added = false; ^ src/protocols/motifs/LigandDiscoverySearch.cc: At global scope: src/protocols/motifs/LigandDiscoverySearch.cc:1383:110: error: no 'bool LigandDiscoverySearch::score_placed_ligand(core::pose::PoseOP&, core::pose::Pose)' member function declared in class 'LigandDiscoverySearch' bool LigandDiscoverySearch::score_placed_ligand(core::pose::PoseOP & minipose, core::pose::Pose original_pose) ^ g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/protocols/jd2/AtomTreeDiffJobOutputter.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/jd2/AtomTreeDiffJobOutputter.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/protocols/jd2/SerializedPoseJobInputter.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/jd2/SerializedPoseJobInputter.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/protocols/jd2/SerializedPoseJobOutputter.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/jd2/SerializedPoseJobOutputter.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/protocols/jobdist/JobDistributors.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/jobdist/JobDistributors.cc cc1plus: all warnings being treated as errors g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/core/init/init.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/init/init.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/utility/crash_report.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/crash_report.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/core/io/mmtf/mmtf_writer.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/io/mmtf/mmtf_writer.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/core/io/pose_to_sfr/PoseToStructFileRepConverter.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/io/pose_to_sfr/PoseToStructFileRepConverter.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/protocols/features/ProtocolFeatures.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/features/ProtocolFeatures.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/protocols/motifs/LigandDiscoverySearch.os] Error 1 scons: building terminated because of errors.
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