Running: /home/benchmark/prefix/nobu-5/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin cxx=gcc extras=cxx11thread,serialization -j64
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/cxx11thread-serialization/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 -DMULTI_THREADED -DSERIALIZATION -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:998:158: error: no matching function for call to 'LigandDiscoverySearch::score_placed_ligand(core::pose::PoseOP&, core::pose::Pose&, std::string&, std::string&, std::string&, std::string&, core::Real&, 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.cc:998:158: note: candidate is:
In file included from src/protocols/motifs/LigandDiscoverySearch.cc:131:0:
src/protocols/motifs/LigandDiscoverySearch.hh:269:7: note: bool LigandDiscoverySearch::score_placed_ligand(core::pose::PoseOP&, core::pose::Pose, std::string&, std::string&, std::string&, std::string&, core::Real&, core::Size&)
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.hh:269:7: note: no known conversion for argument 8 from 'int' to 'core::Size& {aka long unsigned int&}'
src/protocols/motifs/LigandDiscoverySearch.cc:799:9: error: unused variable 'ligand_added' [-Werror=unused-variable]
bool ligand_added = false;
^
src/protocols/motifs/LigandDiscoverySearch.cc: In member function 'bool LigandDiscoverySearch::score_placed_ligand(core::pose::PoseOP&, core::pose::Pose, std::string&, std::string&, std::string&, std::string&, core::Real&, core::Size&)':
src/protocols/motifs/LigandDiscoverySearch.cc:1435:4: error: 'passed_placement_counter' was not declared in this scope
++passed_placement_counter;
^
src/protocols/motifs/LigandDiscoverySearch.cc:1439:41: error: 'ligresOP' was not declared in this scope
working_pose_->append_residue_by_jump(*ligresOP, working_pose_->size(), "", "", true);
^
src/protocols/motifs/LigandDiscoverySearch.cc:1445:174: error: 'trip_atom_1' was not declared in this scope
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: 'working_position' was not declared in this scope
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: 'trip_atom_2' was not declared in this scope
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: 'trip_atom_3' was not declared in this scope
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: 'ligand_added' was not declared in this scope
if ( ligand_added == false ) {
^
src/protocols/motifs/LigandDiscoverySearch.cc:1502:31: error: 'lig_mrt' was not declared in this scope
rts->add_base_residue_type(lig_mrt);
^
src/protocols/motifs/LigandDiscoverySearch.cc:1639:13: error: 'output_prefix' was not declared in this scope
pdb_name = output_prefix + "_ResPos_" + std::to_string(working_position) + "_ResID_" + discovery_position_residue + "_Trio" + std::to_string(i) + "_" + ligresOP->name() + "_motif_" + motifcop->remark();
^
src/protocols/motifs/LigandDiscoverySearch.cc:1639:89: error: 'discovery_position_residue' was not declared in this scope
pdb_name = output_prefix + "_ResPos_" + std::to_string(working_position) + "_ResID_" + discovery_position_residue + "_Trio" + std::to_string(i) + "_" + ligresOP->name() + "_motif_" + motifcop->remark();
^
src/protocols/motifs/LigandDiscoverySearch.cc:1639:143: error: 'i' was not declared in this scope
pdb_name = output_prefix + "_ResPos_" + std::to_string(working_position) + "_ResID_" + discovery_position_residue + "_Trio" + std::to_string(i) + "_" + ligresOP->name() + "_motif_" + motifcop->remark();
^
src/protocols/motifs/LigandDiscoverySearch.cc:1639:185: error: 'motifcop' was not declared in this scope
pdb_name = output_prefix + "_ResPos_" + std::to_string(working_position) + "_ResID_" + discovery_position_residue + "_Trio" + std::to_string(i) + "_" + ligresOP->name() + "_motif_" + motifcop->remark();
^
cc1plus: all warnings being treated as errors
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scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/motifs/LigandDiscoverySearch.os] Error 1
scons: building terminated because of errors.