Test: linux.gcc.cxx11thread.serialization.unit 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20707」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-1     Started at: 2025-04-02 16:20:55     Run time: 0:01:43      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=cxx11thread,serialization -j48 && /home/benchmark/prefix/nobu-1/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py cxx=gcc mode=debug extras=cxx11thread,serialization cat=test -j48 scons: Reading SConscript files ... Running versioning script ... Done. (0.1 seconds) Number of option files updated: 0 Total 4709 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/devel/dna/MotifLoopBuild.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/devel/dna/MotifLoopBuild.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/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 -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/peptide_deriver/PeptideDeriverMarkdownStreamOutputter.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/motifs/IRCollection.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/IRCollection.cc 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 g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/motifs/LigandMotifSearch.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/LigandMotifSearch.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/motifs/motif_utils.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/motif_utils.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/motifs/MotifDnaPacker.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/MotifDnaPacker.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/motifs/MotifSearch.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/MotifSearch.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/motifs/IdentifyLigandMotifs.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/IdentifyLigandMotifs.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/protein_grid/ProteinGrid.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/protein_grid/ProteinGrid.cc In file included from src/protocols/motifs/LigandDiscoverySearch.cc:131:0: src/protocols/motifs/LigandDiscoverySearch.hh:276:2: error: 'ProteinGridOP' in namespace 'protocols::protein_grid' does not name a type protocols::protein_grid::ProteinGridOP clash_pose_grid_; ^ src/protocols/motifs/LigandDiscoverySearch.hh:281:2: error: 'ProteinGridOP' in namespace 'protocols::protein_grid' does not name a type protocols::protein_grid::ProteinGridOP sf_pose_grid_; ^ src/protocols/motifs/LigandDiscoverySearch.cc: In member function 'core::Size LigandDiscoverySearch::discover(std::string)': src/protocols/motifs/LigandDiscoverySearch.cc:757:106: error: 'clash_pose_grid_' was not declared in this scope clash_pose_grid_(new protocols::protein_grid::ProteinGrid(working_pose_, resolution_increase_factor)); ^ src/protocols/motifs/LigandDiscoverySearch.cc:772:159: error: no matching function for call to 'protocols::protein_grid::ProteinGrid::ProteinGrid(core::pose::PoseOP&, core::Real&, utility::vector1<long unsigned int>&, utility::vector1<long unsigned int>&)' clash_pose_grid_(new protocols::protein_grid::ProteinGrid(working_pose_, resolution_increase_factor, binding_pocket_center_xyz, binding_pocket_dimensions)); ^ src/protocols/motifs/LigandDiscoverySearch.cc:772:159: note: candidates are: In file included from src/protocols/motifs/LigandDiscoverySearch.cc:137:0: src/protocols/protein_grid/ProteinGrid.hh:137:2: note: protocols::protein_grid::ProteinGrid::ProteinGrid() ProteinGrid(); ^ src/protocols/protein_grid/ProteinGrid.hh:137:2: note: candidate expects 0 arguments, 4 provided src/protocols/protein_grid/ProteinGrid.hh:65:2: note: protocols::protein_grid::ProteinGrid::ProteinGrid(const protocols::protein_grid::ProteinGrid&) ProteinGrid( ProteinGrid const & other ); ^ src/protocols/protein_grid/ProteinGrid.hh:65:2: note: candidate expects 1 argument, 4 provided src/protocols/protein_grid/ProteinGrid.hh:62:2: note: protocols::protein_grid::ProteinGrid::ProteinGrid(core::pose::PoseOP, core::Real, numeric::xyzVector<int>, utility::vector1<long unsigned int>) ProteinGrid(core::pose::PoseOP in_pose, core::Real resolution, numeric::xyzVector<int> sub_area_center, utility::vector1<core::Size> sub_region_dimensions); ^ src/protocols/protein_grid/ProteinGrid.hh:62:2: note: no known conversion for argument 3 from 'utility::vector1<long unsigned int>' to 'numeric::xyzVector<int>' src/protocols/protein_grid/ProteinGrid.hh:59:2: note: protocols::protein_grid::ProteinGrid::ProteinGrid(core::pose::PoseOP, numeric::xyzVector<int>, utility::vector1<long unsigned int>) ProteinGrid(core::pose::PoseOP in_pose, numeric::xyzVector<int> sub_area_center, utility::vector1<core::Size> sub_region_dimensions); ^ src/protocols/protein_grid/ProteinGrid.hh:59:2: note: candidate expects 3 arguments, 4 provided src/protocols/protein_grid/ProteinGrid.hh:56:2: note: protocols::protein_grid::ProteinGrid::ProteinGrid(core::pose::PoseOP, core::Real) ProteinGrid(core::pose::PoseOP in_pose, core::Real resolution); ^ src/protocols/protein_grid/ProteinGrid.hh:56:2: note: candidate expects 2 arguments, 4 provided src/protocols/protein_grid/ProteinGrid.hh:53:2: note: protocols::protein_grid::ProteinGrid::ProteinGrid(core::pose::PoseOP) ProteinGrid(core::pose::PoseOP in_pose); ^ src/protocols/protein_grid/ProteinGrid.hh:53:2: note: candidate expects 1 argument, 4 provided src/protocols/motifs/LigandDiscoverySearch.cc:772:160: error: 'clash_pose_grid_' was not declared in this scope clash_pose_grid_(new protocols::protein_grid::ProteinGrid(working_pose_, resolution_increase_factor, binding_pocket_center_xyz, binding_pocket_dimensions)); ^ src/protocols/motifs/LigandDiscoverySearch.cc:775:4: error: expected '}' before 'else' else ^ src/protocols/motifs/LigandDiscoverySearch.cc:778:105: error: 'clash_pose_grid_' was not declared in this scope clash_pose_grid_(new protocols::protein_grid::ProteinGrid(working_pose_, resolution_increase_factor)); ^ src/protocols/motifs/LigandDiscoverySearch.cc:781:3: error: 'else' without a previous 'if' else ^ src/protocols/motifs/LigandDiscoverySearch.cc:784:77: error: 'resolution_increase_factor' was not declared in this scope clash_pose_grid_(new protocols::protein_grid::ProteinGrid(working_pose_, resolution_increase_factor)); ^ src/protocols/motifs/LigandDiscoverySearch.cc:784:104: error: 'clash_pose_grid_' was not declared in this scope clash_pose_grid_(new protocols::protein_grid::ProteinGrid(working_pose_, resolution_increase_factor)); ^ src/protocols/motifs/LigandDiscoverySearch.cc:788:59: error: 'clash_pose_grid_' was not declared in this scope sf_pose_grid_(new protocols::protein_grid::ProteinGrid(*clash_pose_grid_)); ^ src/protocols/motifs/LigandDiscoverySearch.cc:788:76: error: 'sf_pose_grid_' was not declared in this scope sf_pose_grid_(new protocols::protein_grid::ProteinGrid(*clash_pose_grid_)); ^ src/protocols/motifs/LigandDiscoverySearch.cc:794:3: error: 'ProteinGridOP' is not a member of 'protocols::protein_grid' protocols::protein_grid::ProteinGridOP working_sf_pose_grid(new protocols::protein_grid::ProteinGrid(*sf_pose_grid_)); ^ src/protocols/motifs/LigandDiscoverySearch.cc:794:42: error: expected ';' before 'working_sf_pose_grid' protocols::protein_grid::ProteinGridOP working_sf_pose_grid(new protocols::protein_grid::ProteinGrid(*sf_pose_grid_)); ^ src/protocols/motifs/LigandDiscoverySearch.cc:800:24: error: 'working_sf_pose_grid' was not declared in this scope occupied_ratios[1] = working_sf_pose_grid->get_grid_occupied_cell_ratio(); ^ src/protocols/motifs/LigandDiscoverySearch.cc:932:54: error: 'working_position' was not declared in this scope motifcop->place_residue( working_pose_->residue(working_position), *ligresOP, trip_atom_1, trip_atom_2, trip_atom_3 , true ); ^ src/protocols/motifs/LigandDiscoverySearch.cc:977:116: error: 'discovery_position_residue' was not declared in this scope std::string matrix_pdb_prefix = 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:1170:105: error: 'discovery_position_residue' was not declared in this scope std::string 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:1243:74: error: 'mymap' was not declared in this scope placement_motifs_data = ilm.evaluate_motifs_of_pose(working_pose_, mymap, pdb_short_unique_name); ^ src/protocols/motifs/LigandDiscoverySearch.cc: At global scope: src/protocols/motifs/LigandDiscoverySearch.cc:1384:2: error: expected unqualified-id before 'return' return 1; ^ src/protocols/motifs/LigandDiscoverySearch.cc:1385:1: error: expected declaration before '}' token } ^ g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/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 -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/jd2/AtomTreeDiffJobOutputter.cc src/protocols/motifs/LigandDiscoverySearch.cc: In member function 'core::Size LigandDiscoverySearch::discover(std::string)': src/protocols/motifs/LigandDiscoverySearch.cc:1383:2: error: control reaches end of non-void function [-Werror=return-type] } ^ g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/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 -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/jd2/SerializedPoseJobInputter.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/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 -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/jd2/SerializedPoseJobOutputter.cc cc1plus: all warnings being treated as errors g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/jd2/archive/ArchiveManager.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/jd2/archive/ArchiveManager.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/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 -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/jobdist/JobDistributors.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/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 -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/core/init/init.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/basic/options/option.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 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build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/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 -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/features/ProtocolFeatures.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/motif_tools/extract_motifs.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 -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/apps/public/motif_tools/extract_motifs.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/motif_tools/incorporate_motifs.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 -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/apps/public/motif_tools/incorporate_motifs.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/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 -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/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/nmr/ligand_transform_with_pcs.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 -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/apps/public/nmr/ligand_transform_with_pcs.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/motif_ligand_discovery/remove_duplicate_motifs.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 -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/apps/public/motif_ligand_discovery/remove_duplicate_motifs.cc scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/motifs/LigandDiscoverySearch.os] Error 1 In file included from src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc:126:0: src/protocols/motifs/LigandDiscoverySearch.hh:276:2: error: 'ProteinGridOP' in namespace 'protocols::protein_grid' does not name a type protocols::protein_grid::ProteinGridOP clash_pose_grid_; ^ src/protocols/motifs/LigandDiscoverySearch.hh:281:2: error: 'ProteinGridOP' in namespace 'protocols::protein_grid' does not name a type protocols::protein_grid::ProteinGridOP sf_pose_grid_; ^ scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.o] Error 1 scons: building terminated because of errors.
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