Test: mac.clang.python39.integration 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20553」
Test files: 「file-system-view」 「file-list-view」
Daemon: hikaru-2     Started at: 2024-10-07 18:10:56     Run time: 0:00:43      State: build failed


Test Log

Compiling: find bin -type l ! -name ".*" -exec rm {} \; ; /Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python-3.9.clang/707eb77cedeac3e91130adc5f9ccf882/bin/python3.9 ./scons.py bin mode=release cxx=clang extras= -j32 scons: Reading SConscript files ... Running versioning script ... Done. (0.2 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/macos/12.6/64/x86/clang/14.0/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 -isystem /usr/local/include -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 -Winconsistent-missing-override -Wcomma -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -Wno-implicit-function-declaration -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/macos/64/clang/14.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos src/protocols/peptide_deriver/PeptideDeriverMarkdownStreamOutputter.cc clang++ -o build/src/release/macos/12.6/64/x86/clang/14.0/default/protocols/motifs/IdentifyLigandMotifs.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -isystem /usr/local/include -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 -Winconsistent-missing-override -Wcomma -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -Wno-implicit-function-declaration -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/macos/64/clang/14.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos src/protocols/motifs/IdentifyLigandMotifs.cc src/protocols/motifs/IdentifyLigandMotifs.cc:607:41: error: assigning to 'std::map<double, unsigned long>::mapped_type' (aka 'unsigned long') from incompatible type 'utility::vector1<unsigned long>' distance_sorter[closest_distance] = motif_position; ^~~~~~~~~~~~~~ src/protocols/motifs/IdentifyLigandMotifs.cc:634:41: error: unexpected ';' before ')' for ( auto top_trip_pos : top_triplets; ) { ^ src/protocols/motifs/IdentifyLigandMotifs.cc:775:31: error: expected ';' in 'for' statement specifier for ( auto sig_res_pos = 1 : mandatory_residues_for_motifs ){ ^ src/protocols/motifs/IdentifyLigandMotifs.cc:775:31: error: expected expression 4 errors generated. clang++ -o build/src/release/macos/12.6/64/x86/clang/14.0/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 -isystem /usr/local/include -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 -Winconsistent-missing-override -Wcomma -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -Wno-implicit-function-declaration -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/macos/64/clang/14.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos src/protocols/jd2/AtomTreeDiffJobOutputter.cc clang++ -o build/src/release/macos/12.6/64/x86/clang/14.0/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 -isystem /usr/local/include -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 -Winconsistent-missing-override -Wcomma -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -Wno-implicit-function-declaration -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/macos/64/clang/14.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos src/protocols/jd2/SerializedPoseJobInputter.cc clang++ -o build/src/release/macos/12.6/64/x86/clang/14.0/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 -isystem /usr/local/include -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 -Winconsistent-missing-override -Wcomma -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -Wno-implicit-function-declaration -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/macos/64/clang/14.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos src/protocols/jd2/SerializedPoseJobOutputter.cc clang++ -o build/src/release/macos/12.6/64/x86/clang/14.0/default/protocols/jobdist/JobDistributors.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -isystem /usr/local/include -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 -Winconsistent-missing-override -Wcomma -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -Wno-implicit-function-declaration -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/macos/64/clang/14.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos src/protocols/jobdist/JobDistributors.cc clang++ -o build/src/release/macos/12.6/64/x86/clang/14.0/default/core/init/init.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -isystem /usr/local/include -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 -Winconsistent-missing-override -Wcomma -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -Wno-implicit-function-declaration -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/macos/64/clang/14.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos src/core/init/init.cc clang++ -o build/src/release/macos/12.6/64/x86/clang/14.0/default/utility/crash_report.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -isystem /usr/local/include -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 -Winconsistent-missing-override -Wcomma -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -Wno-implicit-function-declaration -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/macos/64/clang/14.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos src/utility/crash_report.cc clang++ -o build/src/release/macos/12.6/64/x86/clang/14.0/default/core/io/mmtf/mmtf_writer.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -isystem /usr/local/include -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 -Winconsistent-missing-override -Wcomma -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -Wno-implicit-function-declaration -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/macos/64/clang/14.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos src/core/io/mmtf/mmtf_writer.cc clang++ -o build/src/release/macos/12.6/64/x86/clang/14.0/default/core/io/pose_to_sfr/PoseToStructFileRepConverter.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -isystem /usr/local/include -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 -Winconsistent-missing-override -Wcomma -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -Wno-implicit-function-declaration -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/macos/64/clang/14.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos src/core/io/pose_to_sfr/PoseToStructFileRepConverter.cc clang++ -o build/src/release/macos/12.6/64/x86/clang/14.0/default/protocols/features/ProtocolFeatures.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -isystem /usr/local/include -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 -Winconsistent-missing-override -Wcomma -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -Wno-implicit-function-declaration -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/macos/64/clang/14.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos src/protocols/features/ProtocolFeatures.cc clang++ -o build/src/release/macos/12.6/64/x86/clang/14.0/default/apps/public/motif_ligand_discovery/determine_real_motifs.o -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -isystem /usr/local/include -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 -Winconsistent-missing-override -Wcomma -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -Wno-implicit-function-declaration -O3 -Wno-unused-variable -Wno-unused-parameter -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/macos/64/clang/14.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos src/apps/public/motif_ligand_discovery/determine_real_motifs.cc src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:56:17: error: no type named 'Tracer' in namespace 'basic' static basic::Tracer ms_tr( "determine_real_motifs", basic::t_info ); ~~~~~~~^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:56:63: error: no member named 't_info' in namespace 'basic' static basic::Tracer ms_tr( "determine_real_motifs", basic::t_info ); ~~~~~~~^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:58:19: error: expected namespace name using namespace options; ^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:59:19: error: expected namespace name using namespace OptionKeys; ^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:67:11: error: no template named 'vector1'; did you mean 'utility::vector1'? typedef vector1< utility::file::FileName > Filenames; ^~~~~~~ utility::vector1 src/utility/vector1.hh:42:7: note: 'utility::vector1' declared here class vector1 : ^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:71:8: error: use of undeclared identifier 'option'; did you mean 'optind'? if ( option[ in::file::l ].user() ) { ^~~~~~ optind /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/unistd.h:512:12: note: 'optind' declared here extern int optind, opterr, optopt; ^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:71:16: error: use of undeclared identifier 'in' if ( option[ in::file::l ].user() ) { ^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:72:25: error: use of undeclared identifier 'option'; did you mean 'optind'? Filenames listnames( option[ in::file::l ]().vector() ); ^~~~~~ optind /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/unistd.h:512:12: note: 'optind' declared here extern int optind, opterr, optopt; ^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:72:33: error: use of undeclared identifier 'in' Filenames listnames( option[ in::file::l ]().vector() ); ^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:83:15: error: use of undeclared identifier 'option'; did you mean 'optind'? } else if ( option[ in::file::s ].user() ) { ^~~~~~ optind /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/unistd.h:512:12: note: 'optind' declared here extern int optind, opterr, optopt; ^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:83:23: error: use of undeclared identifier 'in' } else if ( option[ in::file::s ].user() ) { ^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:84:23: error: use of undeclared identifier 'in' pdbnames = option[ in::file::s ]().vector(); ^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:84:15: error: use of undeclared identifier 'option'; did you mean 'optind'? pdbnames = option[ in::file::s ]().vector(); ^~~~~~ optind /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/unistd.h:512:12: note: 'optind' declared here extern int optind, opterr, optopt; ^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:103:50: error: non-const lvalue reference to type 'protocols::motifs::MotifCOPs' (aka 'vector1<shared_ptr<const protocols::motifs::Motif>>') cannot bind to a value of unrelated type 'protocols::motifs::MotifLibrary' protocols::motifs::hash_motif_library_into_map(real_motifs,hashed_real_library); ^~~~~~~~~~~ src/protocols/motifs/motif_utils.hh:281:65: note: passing argument to parameter 'input_library' here void hash_motif_library_into_map(protocols::motifs::MotifCOPs & input_library, std::map<motif_atoms, protocols::motifs::MotifCOPs> & mymap); ^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:111:25: error: no member named 'file_exists' in namespace 'utility::file' if ( !utility::file::file_exists( *filename ) ) { ~~~~~~~~~~~~~~~^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:117:41: error: use of undeclared identifier 'string_split' std::string pdbprefix( string_split( string_split( *filename, '/' ).back(), '.' ).front() ); ^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:121:10: error: no member named 'import_pose' in namespace 'core' core::import_pose::pose_from_file( pose_pointer_helper, *filename , core::import_pose::PDB_file); ~~~~~~^ src/apps/public/motif_ligand_discovery/determine_real_motifs.cc:121:78: error: no member named 'import_pose' in namespace 'core' core::import_pose::pose_from_file( pose_pointer_helper, *filename , core::import_pose::PDB_file); ~~~~~~^ 18 errors generated. scons: *** [build/src/release/macos/12.6/64/x86/clang/14.0/default/protocols/motifs/IdentifyLigandMotifs.os] Error 1 scons: *** [build/src/release/macos/12.6/64/x86/clang/14.0/default/apps/public/motif_ligand_discovery/determine_real_motifs.o] Error 1 scons: building terminated because of errors.

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