Running: /Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python-3.9.clang/707eb77cedeac3e91130adc5f9ccf882/bin/python3.9 ./scons.py bin 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/debug/macos/12.6/64/x86/clang/14.0/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 -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -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/LigandDiscoverySearch.cc
src/protocols/motifs/LigandDiscoverySearch.cc:998:142: error: non-const lvalue reference to type 'core::Size' (aka 'unsigned long') cannot bind to a value of unrelated type 'int'
if(score_placed_ligand(minipose, original_pose, pdb_name, pdb_short_unique_name, comment_table_header, comment_table_data, delta_score, clashing_counter))
^~~~~~~~~~~~~~~~
src/protocols/motifs/LigandDiscoverySearch.hh:269:260: note: passing argument to parameter 'clashing_counter' here
bool score_placed_ligand(core::pose::PoseOP & minipose, core::pose::Pose original_pose, std::string & pdb_name, std::string & pdb_short_unique_name, std::string & comment_table_header, std::string & comment_table_data, core::Real & delta_score, core::Size & clashing_counter);
^
src/protocols/motifs/LigandDiscoverySearch.cc:1435:4: error: use of undeclared identifier 'passed_placement_counter'
++passed_placement_counter;
^
src/protocols/motifs/LigandDiscoverySearch.cc:1439:41: error: use of undeclared identifier 'ligresOP'
working_pose_->append_residue_by_jump(*ligresOP, working_pose_->size(), "", "", true);
^
src/protocols/motifs/LigandDiscoverySearch.cc:1445:174: error: use of undeclared identifier 'trip_atom_1'
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_1, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_1 ), fx1 ) ) );
^
src/protocols/motifs/LigandDiscoverySearch.cc:1445:254: error: use of undeclared identifier 'working_position'
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_1, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_1 ), fx1 ) ) );
^
src/protocols/motifs/LigandDiscoverySearch.cc:1445:298: error: use of undeclared identifier 'ligresOP'
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_1, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_1 ), fx1 ) ) );
^
src/protocols/motifs/LigandDiscoverySearch.cc:1445:313: error: use of undeclared identifier 'trip_atom_1'
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_1, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_1 ), fx1 ) ) );
^
src/protocols/motifs/LigandDiscoverySearch.cc:1448:174: error: use of undeclared identifier 'trip_atom_2'
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_2, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_2 ), fx2 ) ) );
^
src/protocols/motifs/LigandDiscoverySearch.cc:1448:254: error: use of undeclared identifier 'working_position'
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_2, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_2 ), fx2 ) ) );
^
src/protocols/motifs/LigandDiscoverySearch.cc:1448:298: error: use of undeclared identifier 'ligresOP'
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_2, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_2 ), fx2 ) ) );
^
src/protocols/motifs/LigandDiscoverySearch.cc:1448:313: error: use of undeclared identifier 'trip_atom_2'
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_2, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_2 ), fx2 ) ) );
^
src/protocols/motifs/LigandDiscoverySearch.cc:1451:174: error: use of undeclared identifier 'trip_atom_3'
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_3, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_3 ), fx3 ) ) );
^
src/protocols/motifs/LigandDiscoverySearch.cc:1451:254: error: use of undeclared identifier 'working_position'
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_3, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_3 ), fx3 ) ) );
^
src/protocols/motifs/LigandDiscoverySearch.cc:1451:298: error: use of undeclared identifier 'ligresOP'
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_3, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_3 ), fx3 ) ) );
^
src/protocols/motifs/LigandDiscoverySearch.cc:1451:313: error: use of undeclared identifier 'trip_atom_3'
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_3, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_3 ), fx3 ) ) );
^
src/protocols/motifs/LigandDiscoverySearch.cc:1488:7: error: use of undeclared identifier 'ligand_added'
if ( ligand_added == false ) {
^
src/protocols/motifs/LigandDiscoverySearch.cc:1489:3: error: use of undeclared identifier 'ligand_added'
ligand_added = true;
^
src/protocols/motifs/LigandDiscoverySearch.cc:1502:31: error: use of undeclared identifier 'lig_mrt'
rts->add_base_residue_type(lig_mrt);
^
src/protocols/motifs/LigandDiscoverySearch.cc:1639:13: error: use of undeclared identifier 'output_prefix'
pdb_name = output_prefix + "_ResPos_" + std::to_string(working_position) + "_ResID_" + discovery_position_residue + "_Trio" + std::to_string(i) + "_" + ligresOP->name() + "_motif_" + motifcop->remark();
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
clang++ -o build/src/debug/macos/12.6/64/x86/clang/14.0/default/libutility.dylib -dynamiclib -install_name /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/src/debug/macos/12.6/64/x86/clang/14.0/default/libutility.dylib -stdlib=libc++ build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/backtrace.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/Binary_Util.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/crash_report.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/CSI_Sequence.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/curl.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/dating.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/exit.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/heap.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/inline_file_provider.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/integer_mapping.os 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build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/sql_database/types.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/tag/Tag.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/tag/util.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/tag/XMLSchemaGeneration.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/tag/XMLSchemaValidation.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/thread/ReadWriteMutex.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/utility/xsd_util/util.os -Lexternal/lib -Lbuild/src/debug/macos/12.6/64/x86/clang/14.0/default -Lsrc -Lbuild/external/debug/macos/12.6/64/x86/clang/14.0/default -Lexternal -L/usr/lib -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
scons: *** [build/src/debug/macos/12.6/64/x86/clang/14.0/default/protocols/motifs/LigandDiscoverySearch.os] Error 1
scons: building terminated because of errors.