Test: linux.clang.build.release 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20516」
Test files: 「file-system-view」 「file-list-view」
Daemon: hojo-4     Started at: 2024-09-24 16:50:13     Run time: 0:02:00      State: failed


Running: /home/benchmark/prefix/hojo-4/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin cxx=clang extras= mode=release -j24 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 ... 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:987:9: error: use of undeclared identifier 'score_placed_ligand' if(score_placed_ligand(minipose, original_pose)) ^ src/protocols/motifs/LigandDiscoverySearch.cc:1001:46: error: use of undeclared identifier 'pdb_short_unique_name' 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: use of undeclared identifier 'pdb_name' pdb_name = pdb_name + "_motifs_" + std::to_string(motifs_made); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1026:18: error: use of undeclared identifier 'pdb_name' pdb_name = pdb_name + "_motifs_" + std::to_string(motifs_made); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1029:7: error: use of undeclared identifier 'comment_table_data' comment_table_data = comment_table_data + std::to_string(motifs_made) + ","; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1029:28: error: use of undeclared identifier 'comment_table_data' comment_table_data = comment_table_data + std::to_string(motifs_made) + ","; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1113:8: error: use of undeclared identifier 'pdb_name' pdb_name = pdb_name + "_sigmotifs_" + std::to_string(significant_motifs_made); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1113:19: error: use of undeclared identifier 'pdb_name' pdb_name = pdb_name + "_sigmotifs_" + std::to_string(significant_motifs_made); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1118:8: error: use of undeclared identifier 'comment_table_data' comment_table_data = comment_table_data + std::to_string(significant_motifs_made) + ","; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1118:29: error: use of undeclared identifier 'comment_table_data' comment_table_data = comment_table_data + std::to_string(significant_motifs_made) + ","; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1122:8: error: use of undeclared identifier 'comment_table_data' comment_table_data = comment_table_data + ","; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1122:29: error: use of undeclared identifier 'comment_table_data' comment_table_data = comment_table_data + ","; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1244:8: error: use of undeclared identifier 'pdb_name' pdb_name = pdb_name + "_realmotifratio_" + std::to_string(real_looking_motif_ratio); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1244:19: error: use of undeclared identifier 'pdb_name' pdb_name = pdb_name + "_realmotifratio_" + std::to_string(real_looking_motif_ratio); ^ src/protocols/motifs/LigandDiscoverySearch.cc:1248:8: error: use of undeclared identifier 'comment_table_data' comment_table_data = comment_table_data + std::to_string(motifs_that_look_real_real) + "," + std::to_string(real_looking_motif_ratio) + ","; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1248:29: error: use of undeclared identifier 'comment_table_data' comment_table_data = comment_table_data + std::to_string(motifs_that_look_real_real) + "," + std::to_string(real_looking_motif_ratio) + ","; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1253:8: error: use of undeclared identifier 'comment_table_data' comment_table_data = comment_table_data + "," + ","; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1253:29: error: use of undeclared identifier 'comment_table_data' comment_table_data = comment_table_data + "," + ","; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1259:7: error: use of undeclared identifier 'comment_table_data' comment_table_data = comment_table_data + "," + "," + "," + ","; ^ 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/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 build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/sys_util.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/recent_history_queue.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/static_database.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/string_util.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/vector0.srlz.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/vector1.srlz.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/VirtualBase.srlz.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/boinc/boinc_util.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/excn/Exceptions.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/file/file_sys_util.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/file/FileName.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/file/gzip_util.os 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 build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/io/ozstream.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/io/util.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/io/base64.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/io/tarparser.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/keys/Key.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/keys/Key2Tuple.srlz.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/keys/Key3Tuple.srlz.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/keys/Key4Tuple.srlz.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/libsvm/Svm_rosetta.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/libsvm/Svm.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/json_spirit/json_spirit_reader.os build/src/release/linux/5.4/64/x86/clang/3.4/default/utility/json_spirit/json_spirit_value.os 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 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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