Test: linux.gcc.unit 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20554」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-1     Started at: 2024-10-09 17:38:02     Run time: 0:01:14      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= -j48 && /home/benchmark/prefix/nobu-1/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py cxx=gcc mode=debug extras= cat=test -j48 find: ‘bin’: No such file or directory 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/7/default/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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/peptide_deriver/PeptideDeriverMarkdownStreamOutputter.cc g++ -o 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-Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/scoring/LigandScorer.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/sewing/scoring/MotifScorer.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/scoring/MotifScorer.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/sewing/scoring/TopNMotifScorer.os -c -std=c++0x 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-Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/scoring/PartnerMotifScorer.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/sewing/scoring/SubsetPartnerMotifScorer.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/sewing/scoring/SubsetPartnerMotifScorer.cc g++ -o 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-Isrc/platform/linux src/protocols/analysis/PackStatMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/analysis/burial_metrics/PolarGroupBurialPyMolStringMetric.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/analysis/burial_metrics/PolarGroupBurialPyMolStringMetric.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/analysis/simple_metrics/ConstraintsMetric.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/analysis/simple_metrics/ConstraintsMetric.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/analysis/simple_metrics/RunSimpleMetricsMover.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/analysis/simple_metrics/RunSimpleMetricsMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/analysis/simple_metrics/SequenceRecoveryMetric.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/analysis/simple_metrics/SequenceRecoveryMetric.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/monte_carlo/ResetBaselineMover.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/monte_carlo/ResetBaselineMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/monte_carlo/GenericMonteCarloMover.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/monte_carlo/GenericMonteCarloMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/monte_carlo/GenericSimulatedAnnealer.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/monte_carlo/GenericSimulatedAnnealer.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/monte_carlo/MonteCarloInterface.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/monte_carlo/MonteCarloInterface.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/monte_carlo/MonteCarloRecover.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/monte_carlo/MonteCarloRecover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/monte_carlo/MonteCarloTest.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/monte_carlo/MonteCarloTest.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/monte_carlo/MonteCarloReset.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/monte_carlo/MonteCarloReset.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/carbohydrates/CreateGlycanSequonMover.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/carbohydrates/CreateGlycanSequonMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/carbohydrates/GlycanSampler.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/carbohydrates/GlycanSampler.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/carbohydrates/GlycanTreeMinMover.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/carbohydrates/GlycanTreeMinMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/carbohydrates/GlycanTreeModeler.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/carbohydrates/GlycanTreeModeler.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/carbohydrates/LinkageConformerMover.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/carbohydrates/LinkageConformerMover.cc src/protocols/motifs/IdentifyLigandMotifs.cc: In member function 'utility::vector1<double> IdentifyLigandMotifs::evaluate_motifs_of_pose(core::pose::PoseOP, std::__debug::map<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, utility::vector1<std::shared_ptr<const protocols::motifs::Motif> > >, const string&)': src/protocols/motifs/IdentifyLigandMotifs.cc:776:27: error: initializer in range-based 'for' loop for ( auto sig_res_pos = 1 : mandatory_residues_for_motifs ){ ^ g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/carbohydrates/IdealizeAnomericHydrogens.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/carbohydrates/IdealizeAnomericHydrogens.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/carbohydrates/RingPlaneFlipMover.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/carbohydrates/RingPlaneFlipMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/carbohydrates/SimpleGlycosylateMover.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/carbohydrates/SimpleGlycosylateMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/carbohydrates/TautomerizeAnomerMover.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/carbohydrates/TautomerizeAnomerMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/carbohydrates/util.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/carbohydrates/util.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/cutoutdomain/CutOutDomain.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/cutoutdomain/CutOutDomain.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/pb_potential/SetupPoissonBoltzmannPotential.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/pb_potential/SetupPoissonBoltzmannPotential.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/simple_ddg/DdgFilter.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/simple_ddg/DdgFilter.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/simple_ddg/ddG.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/simple_ddg/ddG.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/simple_ddg/AlaScan.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/simple_ddg/AlaScan.cc g++ -o 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src/protocols/calc_taskop_movers/ForceDisulfidesMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/calc_taskop_movers/ConsensusDesignMover.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/calc_taskop_movers/ConsensusDesignMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/calc_taskop_movers/DesignRepackMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem 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-Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/calc_taskop_filters/SigmoidFilter.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/calc_taskop_filters/MultipleSigmoidsFilter.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/calc_taskop_filters/MultipleSigmoidsFilter.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/calc_taskop_filters/OperatorFilter.os 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build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/calc_taskop_filters/RotamerBoltzmannWeight2.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/calc_taskop_filters/RotamerBoltzmannWeight2.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/normalmode/NormalMode.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem 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src/protocols/normalmode/NormalModeMultiFunc.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/normalmode/NormalModeRelaxMover.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/normalmode/NormalModeRelaxMover.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/frag_picker/BestTotalScoreSelector.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem 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-Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/frag_picker/ContactTypes.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/frag_picker/CS2ndShift.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/frag_picker/CS2ndShift.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/frag_picker/CSTalosIO.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem 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-Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/frag_picker/DiversifyCrmsdByClustering.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/frag_picker/DiversifyCrmsdSelector.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/frag_picker/DiversifyCrmsdSelector.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/frag_picker/DiversifyDihedralsSelector.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/frag_picker/DiversifyDihedralsSelector.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/frag_picker/Faraggi_SA.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/frag_picker/Faraggi_SA.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/frag_picker/FragmentCandidate.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/frag_picker/FragmentCandidate.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/frag_picker/FragmentPicker.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/frag_picker/FragmentPicker.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/frag_picker/FragmentScoreFilter.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/frag_picker/FragmentScoreFilter.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/frag_picker/JCouplingIO.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/frag_picker/JCouplingIO.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/frag_picker/LAMBEGO_IO.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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/frag_picker/LAMBEGO_IO.cc scons: *** [build/src/debug/linux/5.4/64/x86/gcc/7/default/protocols/motifs/IdentifyLigandMotifs.os] Error 1 scons: building terminated because of errors.
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