Compiling: find bin -type l ! -name ".*" -exec rm {} \; ; /home/benchmark/prefix/hojo-3/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin mode=debug cxx=clang extras=tensorflow -j24
scons: Reading SConscript files ...
Running versioning script ... Done. (0.1 seconds)
Unknown type:Bool!!!
Updating submodules needed for compilation.
Finished updating ResidueProperty code
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scons: done reading SConscript files.
scons: Building targets ...
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/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 -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/init.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/cartesian_frags/CartesianFragment.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/cartesian_frags/CartesianFragment.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/cartesian_frags/DNA_FragLib.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/cartesian_frags/DNA_FragLib.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/cartesian_frags/dna_util.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/cartesian_frags/dna_util.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/cartesian_frags/SafeID.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/cartesian_frags/SafeID.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/coupled_sidechains/CoupledSidechainProtocol2.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/coupled_sidechains/CoupledSidechainProtocol2.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/cstEnergyBalance/minimalCstRelaxUtil.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/cstEnergyBalance/minimalCstRelaxUtil.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_design/DumpStatsSS.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/denovo_design/DumpStatsSS.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_design/ParametricSheet.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/denovo_design/ParametricSheet.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_design/RestrictRegion.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/denovo_design/RestrictRegion.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_design/calculators/ResidueCentralityCalculator.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/denovo_design/calculators/ResidueCentralityCalculator.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_design/filters/CoreResiduesPerElementFilter.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/denovo_design/filters/CoreResiduesPerElementFilter.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_design/filters/FoldabilityFilter.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/denovo_design/filters/FoldabilityFilter.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_design/scoring/SideChainNeighborsEnergy.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/denovo_design/scoring/SideChainNeighborsEnergy.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_design/task_operations/DesignBySecondaryStructure.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/denovo_design/task_operations/DesignBySecondaryStructure.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_design/task_operations/HighestEnergyRegion.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/denovo_design/task_operations/HighestEnergyRegion.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_protein_design/CreateStartingStructureMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/denovo_protein_design/CreateStartingStructureMover.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_protein_design/DesignRelaxMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/denovo_protein_design/DesignRelaxMover.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_protein_design/SequenceFitnessMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/denovo_protein_design/SequenceFitnessMover.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_protein_design/util.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/denovo_protein_design/util.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/dna/base_movers.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/dna/base_movers.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/dna/ProteinDNA_Relax.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/dna/ProteinDNA_Relax.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/dna/protocols.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/dna/protocols.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/dna/relax_util.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/dna/relax_util.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/dna/MotifLoopBuild.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/dna/MotifLoopBuild.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/dna/util_motif_loop.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/dna/util_motif_loop.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/dna/util.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/dna/util.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/domain_assembly/domain_assembly.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/domain_assembly/domain_assembly.cc
In file included from src/devel/denovo_design/task_operations/HighestEnergyRegion.cc:19:
In file included from src/protocols/denovo_design/calculators/CavityCalculator.hh:25:
In file included from src/core/scoring/packstat/compute_sasa.hh:32:
src/numeric/trig.functions.hh:77:108: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
in_sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/domain_assembly/domain_assembly_setup.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/domain_assembly/domain_assembly_setup.cc
src/numeric/trig.functions.hh:98:105: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
src/numeric/trig.functions.hh:118:64: error: no member named 'keep_beyond_sin_cos_range' in namespace 'basic::options::OptionKeys::run'
if (basic::options::option[ basic::options::OptionKeys::run::keep_beyond_sin_cos_range ]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
In file included from src/devel/denovo_design/task_operations/HighestEnergyRegion.cc:19:
In file included from src/protocols/denovo_design/calculators/CavityCalculator.hh:25:
src/core/scoring/packstat/compute_sasa.hh:172:30: error: no matching function for call to 'sin_cos_range'
PackstatReal p = std::acos( sin_cos_range( diff(3) ) );
^~~~~~~~~~~~~
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/domain_assembly/DomainAssemblyMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/domain_assembly/DomainAssemblyMover.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/domain_assembly/DomainAssemblyReader.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/domain_assembly/DomainAssemblyReader.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/domain_assembly/RedesignDomainAssemblyMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/domain_assembly/RedesignDomainAssemblyMover.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/domain_assembly/DomainAssemblyJobInputter.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/domain_assembly/DomainAssemblyJobInputter.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/domain_insertion/FusePosesNtoCMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/domain_insertion/FusePosesNtoCMover.cc
In file included from src/devel/denovo_protein_design/SequenceFitnessMover.cc:34:
In file included from src/core/scoring/packstat/compute_sasa.hh:32:
src/numeric/trig.functions.hh:77:108: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
in_sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
src/numeric/trig.functions.hh:98:105: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
src/numeric/trig.functions.hh:118:64: error: no member named 'keep_beyond_sin_cos_range' in namespace 'basic::options::OptionKeys::run'
if (basic::options::option[ basic::options::OptionKeys::run::keep_beyond_sin_cos_range ]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
In file included from src/devel/denovo_protein_design/SequenceFitnessMover.cc:34:
src/core/scoring/packstat/compute_sasa.hh:172:30: error: no matching function for call to 'sin_cos_range'
PackstatReal p = std::acos( sin_cos_range( diff(3) ) );
^~~~~~~~~~~~~
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/domain_insertion/InsertionSiteTestMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/domain_insertion/InsertionSiteTestMover.cc
In file included from src/devel/dna/base_movers.cc:26:
In file included from src/core/conformation/find_neighbors.hh:29:
In file included from src/numeric/xyzTriple.hh:30:
src/numeric/trig.functions.hh:77:108: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
in_sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
src/numeric/trig.functions.hh:98:105: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
src/numeric/trig.functions.hh:118:64: error: no member named 'keep_beyond_sin_cos_range' in namespace 'basic::options::OptionKeys::run'
if (basic::options::option[ basic::options::OptionKeys::run::keep_beyond_sin_cos_range ]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/enzdes/DesignSilentStruct.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/enzdes/DesignSilentStruct.cc
In file included from src/devel/dna/relax_util.cc:39:
In file included from src/numeric/xyz.functions.hh:23:
src/numeric/trig.functions.hh:77:108: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
in_sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
src/numeric/trig.functions.hh:98:105: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/enzdes/EnzdesRemodelProtocol.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/enzdes/EnzdesRemodelProtocol.cc
src/numeric/trig.functions.hh:118:64: error: no member named 'keep_beyond_sin_cos_range' in namespace 'basic::options::OptionKeys::run'
if (basic::options::option[ basic::options::OptionKeys::run::keep_beyond_sin_cos_range ]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/fold_from_loops/FoldFromLoops_functions.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/fold_from_loops/FoldFromLoops_functions.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/fold_from_loops/FoldFromLoopsMover.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/fold_from_loops/FoldFromLoopsMover.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/inv_kin_lig_loop_design/Cloner.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/inv_kin_lig_loop_design/Cloner.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/inv_kin_lig_loop_design/JumpManager.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/inv_kin_lig_loop_design/JumpManager.cc
clang++ -o build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/inv_kin_lig_loop_design/Loop.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DUSE_TENSORFLOW -DUSE_TENSORFLOW_CPU -Isrc -Iexternal/include -Isrc/platform/linux/64/clang/3.4 -Isrc/platform/linux/64/clang -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/inv_kin_lig_loop_design/Loop.cc
4 errors generated.
scons: *** [build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_protein_design/SequenceFitnessMover.os] Error 1
In file included from src/devel/dna/relax_util.cc:39:
src/numeric/xyz.functions.hh:306:21: error: no matching function for call to 'sin_cos_range'
angle = std::acos( sin_cos_range( dot(a, b) ) );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:324:2: note: in instantiation of function template specialization 'numeric::angle_radians<double>' requested here
angle_radians( p1, p2, p3, angle );
^
src/numeric/xyz.functions.hh:332:43: note: in instantiation of function template specialization 'numeric::angle_radians<double>' requested here
xyzVector< double > const & p3) { return angle_radians(p1, p2, p3); }
^
src/numeric/xyz.functions.hh:349:2: error: no matching function for call to 'angle_radians'
angle_radians( p1, p2, p3, angle );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:357:43: note: in instantiation of function template specialization 'numeric::angle_degrees<double>' requested here
xyzVector< double > const & p3) { return angle_degrees(p1, p2, p3); }
^
src/numeric/xyz.functions.hh:294:1: note: candidate template ignored: substitution failure [with T = double]
angle_radians(
^
src/numeric/xyz.functions.hh:367:1: note: candidate template ignored: could not match 'xyzVector<type-parameter-0-0>' against 'double'
angle_radians(
^
src/numeric/xyz.functions.hh:317:1: note: candidate function template not viable: requires 3 arguments, but 4 were provided
angle_radians(
^
src/numeric/xyz.functions.hh:377:23: error: no matching function for call to 'sin_cos_range'
T angle = std::acos( sin_cos_range( dot(a, b) ) );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:386:43: note: in instantiation of function template specialization 'numeric::angle_radians<double>' requested here
xyzVector< double > const & p4) { return angle_radians(p1, p2, p3, p4); }
^
src/numeric/xyz.functions.hh:403:12: error: no matching function for call to 'angle_radians'
T angle = angle_radians( p1, p2, p3, p4 );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:412:43: note: in instantiation of function template specialization 'numeric::angle_degrees<double>' requested here
xyzVector< double > const & p4) { return angle_degrees(p1, p2, p3, p4); }
^
src/numeric/xyz.functions.hh:294:1: note: candidate template ignored: deduced conflicting types for parameter 'T' ('double' vs. 'const numeric::xyzVector<double>')
angle_radians(
^
src/numeric/xyz.functions.hh:367:1: note: candidate template ignored: substitution failure [with T = double]
angle_radians(
^
src/numeric/xyz.functions.hh:317:1: note: candidate function template not viable: requires 3 arguments, but 4 were provided
angle_radians(
^
7 errors generated.
scons: *** [build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/dna/relax_util.os] Error 1
4 errors generated.
scons: *** [build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/denovo_design/task_operations/HighestEnergyRegion.os] Error 1
3 errors generated.
scons: *** [build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/dna/base_movers.os] Error 1
In file included from src/devel/domain_insertion/InsertionSiteTestMover.cc:43:
In file included from src/core/scoring/rms_util.tmpl.hh:24:
In file included from src/core/conformation/symmetry/SymmetricConformation.hh:24:
In file included from src/core/conformation/symmetry/SymmetryTransform.hh:28:
In file included from src/numeric/HomogeneousTransform.hh:28:
In file included from src/numeric/xyz.functions.hh:23:
src/numeric/trig.functions.hh:77:108: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
in_sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
src/numeric/trig.functions.hh:98:105: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
src/numeric/trig.functions.hh:118:64: error: no member named 'keep_beyond_sin_cos_range' in namespace 'basic::options::OptionKeys::run'
if (basic::options::option[ basic::options::OptionKeys::run::keep_beyond_sin_cos_range ]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
In file included from src/devel/fold_from_loops/FoldFromLoopsMover.cc:26:
In file included from src/core/scoring/rms_util.tmpl.hh:24:
In file included from src/core/conformation/symmetry/SymmetricConformation.hh:24:
In file included from src/core/conformation/symmetry/SymmetryTransform.hh:28:
In file included from src/numeric/HomogeneousTransform.hh:28:
In file included from src/numeric/xyz.functions.hh:23:
src/numeric/trig.functions.hh:77:108: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
in_sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
src/numeric/trig.functions.hh:98:105: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
src/numeric/trig.functions.hh:118:64: error: no member named 'keep_beyond_sin_cos_range' in namespace 'basic::options::OptionKeys::run'
if (basic::options::option[ basic::options::OptionKeys::run::keep_beyond_sin_cos_range ]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
In file included from src/devel/inv_kin_lig_loop_design/JumpManager.cc:31:
In file included from src/numeric/xyz.functions.hh:23:
src/numeric/trig.functions.hh:77:108: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
in_sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
src/numeric/trig.functions.hh:98:105: error: no member named 'sin_cos_range_tolerance' in namespace 'basic::options::OptionKeys::run'
sin_cos_range( T const & x, T const & tol = T( basic::options::option[ basic::options::OptionKeys::run::sin_cos_range_tolerance ] ) )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
src/numeric/trig.functions.hh:118:64: error: no member named 'keep_beyond_sin_cos_range' in namespace 'basic::options::OptionKeys::run'
if (basic::options::option[ basic::options::OptionKeys::run::keep_beyond_sin_cos_range ]) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
In file included from src/devel/inv_kin_lig_loop_design/JumpManager.cc:31:
src/numeric/xyz.functions.hh:306:21: error: no matching function for call to 'sin_cos_range'
angle = std::acos( sin_cos_range( dot(a, b) ) );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:324:2: note: in instantiation of function template specialization 'numeric::angle_radians<double>' requested here
angle_radians( p1, p2, p3, angle );
^
src/numeric/xyz.functions.hh:332:43: note: in instantiation of function template specialization 'numeric::angle_radians<double>' requested here
xyzVector< double > const & p3) { return angle_radians(p1, p2, p3); }
^
src/numeric/xyz.functions.hh:349:2: error: no matching function for call to 'angle_radians'
angle_radians( p1, p2, p3, angle );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:357:43: note: in instantiation of function template specialization 'numeric::angle_degrees<double>' requested here
xyzVector< double > const & p3) { return angle_degrees(p1, p2, p3); }
^
src/numeric/xyz.functions.hh:294:1: note: candidate template ignored: substitution failure [with T = double]
angle_radians(
^
src/numeric/xyz.functions.hh:367:1: note: candidate template ignored: could not match 'xyzVector<type-parameter-0-0>' against 'double'
angle_radians(
^
src/numeric/xyz.functions.hh:317:1: note: candidate function template not viable: requires 3 arguments, but 4 were provided
angle_radians(
^
src/numeric/xyz.functions.hh:377:23: error: no matching function for call to 'sin_cos_range'
T angle = std::acos( sin_cos_range( dot(a, b) ) );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:386:43: note: in instantiation of function template specialization 'numeric::angle_radians<double>' requested here
xyzVector< double > const & p4) { return angle_radians(p1, p2, p3, p4); }
^
src/numeric/xyz.functions.hh:403:12: error: no matching function for call to 'angle_radians'
T angle = angle_radians( p1, p2, p3, p4 );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:412:43: note: in instantiation of function template specialization 'numeric::angle_degrees<double>' requested here
xyzVector< double > const & p4) { return angle_degrees(p1, p2, p3, p4); }
^
src/numeric/xyz.functions.hh:294:1: note: candidate template ignored: deduced conflicting types for parameter 'T' ('double' vs. 'const numeric::xyzVector<double>')
angle_radians(
^
src/numeric/xyz.functions.hh:367:1: note: candidate template ignored: substitution failure [with T = double]
angle_radians(
^
src/numeric/xyz.functions.hh:317:1: note: candidate function template not viable: requires 3 arguments, but 4 were provided
angle_radians(
^
In file included from src/devel/domain_insertion/InsertionSiteTestMover.cc:43:
In file included from src/core/scoring/rms_util.tmpl.hh:24:
In file included from src/core/conformation/symmetry/SymmetricConformation.hh:24:
In file included from src/core/conformation/symmetry/SymmetryTransform.hh:28:
In file included from src/numeric/HomogeneousTransform.hh:28:
src/numeric/xyz.functions.hh:306:21: error: no matching function for call to 'sin_cos_range'
angle = std::acos( sin_cos_range( dot(a, b) ) );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:324:2: note: in instantiation of function template specialization 'numeric::angle_radians<double>' requested here
angle_radians( p1, p2, p3, angle );
^
src/numeric/xyz.functions.hh:332:43: note: in instantiation of function template specialization 'numeric::angle_radians<double>' requested here
xyzVector< double > const & p3) { return angle_radians(p1, p2, p3); }
^
src/numeric/xyz.functions.hh:349:2: error: no matching function for call to 'angle_radians'
angle_radians( p1, p2, p3, angle );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:357:43: note: in instantiation of function template specialization 'numeric::angle_degrees<double>' requested here
xyzVector< double > const & p3) { return angle_degrees(p1, p2, p3); }
^
src/numeric/xyz.functions.hh:294:1: note: candidate template ignored: substitution failure [with T = double]
angle_radians(
^
src/numeric/xyz.functions.hh:367:1: note: candidate template ignored: could not match 'xyzVector<type-parameter-0-0>' against 'double'
angle_radians(
^
src/numeric/xyz.functions.hh:317:1: note: candidate function template not viable: requires 3 arguments, but 4 were provided
angle_radians(
^
src/numeric/xyz.functions.hh:377:23: error: no matching function for call to 'sin_cos_range'
T angle = std::acos( sin_cos_range( dot(a, b) ) );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:386:43: note: in instantiation of function template specialization 'numeric::angle_radians<double>' requested here
xyzVector< double > const & p4) { return angle_radians(p1, p2, p3, p4); }
^
src/numeric/xyz.functions.hh:403:12: error: no matching function for call to 'angle_radians'
T angle = angle_radians( p1, p2, p3, p4 );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:412:43: note: in instantiation of function template specialization 'numeric::angle_degrees<double>' requested here
xyzVector< double > const & p4) { return angle_degrees(p1, p2, p3, p4); }
^
src/numeric/xyz.functions.hh:294:1: note: candidate template ignored: deduced conflicting types for parameter 'T' ('double' vs. 'const numeric::xyzVector<double>')
angle_radians(
^
src/numeric/xyz.functions.hh:367:1: note: candidate template ignored: substitution failure [with T = double]
angle_radians(
^
src/numeric/xyz.functions.hh:317:1: note: candidate function template not viable: requires 3 arguments, but 4 were provided
angle_radians(
^
In file included from src/devel/fold_from_loops/FoldFromLoopsMover.cc:26:
In file included from src/core/scoring/rms_util.tmpl.hh:24:
In file included from src/core/conformation/symmetry/SymmetricConformation.hh:24:
In file included from src/core/conformation/symmetry/SymmetryTransform.hh:28:
In file included from src/numeric/HomogeneousTransform.hh:28:
src/numeric/xyz.functions.hh:306:21: error: no matching function for call to 'sin_cos_range'
angle = std::acos( sin_cos_range( dot(a, b) ) );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:324:2: note: in instantiation of function template specialization 'numeric::angle_radians<double>' requested here
angle_radians( p1, p2, p3, angle );
^
src/numeric/xyz.functions.hh:332:43: note: in instantiation of function template specialization 'numeric::angle_radians<double>' requested here
xyzVector< double > const & p3) { return angle_radians(p1, p2, p3); }
^
src/numeric/xyz.functions.hh:349:2: error: no matching function for call to 'angle_radians'
angle_radians( p1, p2, p3, angle );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:357:43: note: in instantiation of function template specialization 'numeric::angle_degrees<double>' requested here
xyzVector< double > const & p3) { return angle_degrees(p1, p2, p3); }
^
src/numeric/xyz.functions.hh:294:1: note: candidate template ignored: substitution failure [with T = double]
angle_radians(
^
src/numeric/xyz.functions.hh:367:1: note: candidate template ignored: could not match 'xyzVector<type-parameter-0-0>' against 'double'
angle_radians(
^
src/numeric/xyz.functions.hh:317:1: note: candidate function template not viable: requires 3 arguments, but 4 were provided
angle_radians(
^
src/numeric/xyz.functions.hh:377:23: error: no matching function for call to 'sin_cos_range'
T angle = std::acos( sin_cos_range( dot(a, b) ) );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:386:43: note: in instantiation of function template specialization 'numeric::angle_radians<double>' requested here
xyzVector< double > const & p4) { return angle_radians(p1, p2, p3, p4); }
^
src/numeric/xyz.functions.hh:403:12: error: no matching function for call to 'angle_radians'
T angle = angle_radians( p1, p2, p3, p4 );
^~~~~~~~~~~~~
src/numeric/xyz.functions.hh:412:43: note: in instantiation of function template specialization 'numeric::angle_degrees<double>' requested here
xyzVector< double > const & p4) { return angle_degrees(p1, p2, p3, p4); }
^
src/numeric/xyz.functions.hh:294:1: note: candidate template ignored: deduced conflicting types for parameter 'T' ('double' vs. 'const numeric::xyzVector<double>')
angle_radians(
^
src/numeric/xyz.functions.hh:367:1: note: candidate template ignored: substitution failure [with T = double]
angle_radians(
^
src/numeric/xyz.functions.hh:317:1: note: candidate function template not viable: requires 3 arguments, but 4 were provided
angle_radians(
^
7 errors generated.
scons: *** [build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/inv_kin_lig_loop_design/JumpManager.os] Error 1
7 errors generated.
scons: *** [build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/domain_insertion/InsertionSiteTestMover.os] Error 1
7 errors generated.
scons: *** [build/src/debug/linux/5.4/64/x86/clang/3.4/tensorflow/devel/fold_from_loops/FoldFromLoopsMover.os] Error 1
scons: building terminated because of errors.