Test: mac.clang.unit 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20705」
Test files: 「file-system-view」 「file-list-view」
Daemon: hikaru-2     Started at: 2025-04-01 16:06:17     Run time: 0:00:50      State: build failed


Compiling: find bin -type l ! -name ".*" -exec rm {} \; ; /Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python-3.9.clang/707eb77cedeac3e91130adc5f9ccf882/bin/python3.9 ./scons.py bin mode=debug cxx=clang extras= -j32 && /Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python-3.9.clang/707eb77cedeac3e91130adc5f9ccf882/bin/python3.9 ./scons.py cxx=clang mode=debug extras= cat=test -j32 scons: Reading SConscript files ... Running versioning script ... Done. (0.2 seconds) Number of option files updated: 0 Total 4710 options. Updating submodules needed for compilation. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... clang++ -o build/src/debug/macos/12.6/64/x86/clang/14.0/default/protocols/protein_grid/ProteinGrid.os -c -std=c++11 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -isystem /usr/local/include -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -Winconsistent-missing-override -Wcomma -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -Wno-implicit-function-declaration -O0 -g -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -Isrc -Iexternal/include -Isrc/platform/macos/64/clang/14.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos src/protocols/protein_grid/ProteinGrid.cc src/protocols/protein_grid/ProteinGrid.cc:966:18: error: use of undeclared identifier 'base_10_to_base_62' atom_name = base_10_to_base_62(total_atom_counter); ^ src/protocols/protein_grid/ProteinGrid.cc:1023:38: error: use of undeclared identifier 'Vector' my_mrt.set_ideal_xyz(atom_name, Vector(atom_xyz[1],atom_xyz[2],atom_xyz[3]) ); ^ src/protocols/protein_grid/ProteinGrid.cc:1069:8: error: unknown type name 'ResidueTypeCOP'; did you mean 'core::chemical::ResidueTypeCOP'? ResidueTypeCOP my_rt(ResidueType::make(my_mrt)); ^~~~~~~~~~~~~~ core::chemical::ResidueTypeCOP src/core/chemical/ResidueType.fwd.hh:42:61: note: 'core::chemical::ResidueTypeCOP' declared here typedef utility::pointer::shared_ptr< ResidueType const > ResidueTypeCOP; ^ src/protocols/protein_grid/ProteinGrid.cc:1069:29: error: use of undeclared identifier 'ResidueType'; did you mean 'core::chemical::ResidueType'? ResidueTypeCOP my_rt(ResidueType::make(my_mrt)); ^~~~~~~~~~~ core::chemical::ResidueType src/core/chemical/ResidueType.hh:124:7: note: 'core::chemical::ResidueType' declared here class ResidueType : public ResidueTypeBase, public utility::pointer::enable_shared_from_this< ResidueType > ^ src/protocols/protein_grid/ProteinGrid.cc:1072:66: error: no member named 'ResidueFactory' in namespace 'core::conformation' core::conformation::ResidueOP my_res( core::conformation::ResidueFactory::create_residue(*my_rt)); ~~~~~~~~~~~~~~~~~~~~^ src/protocols/protein_grid/ProteinGrid.cc:1072:44: error: parentheses were disambiguated as a function declaration [-Werror,-Wvexing-parse] core::conformation::ResidueOP my_res( core::conformation::ResidueFactory::create_residue(*my_rt)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/protocols/protein_grid/ProteinGrid.cc:1072:46: note: add a pair of parentheses to declare a variable core::conformation::ResidueOP my_res( core::conformation::ResidueFactory::create_residue(*my_rt)); ^ ( src/protocols/protein_grid/ProteinGrid.cc:1109:16: error: use of undeclared identifier 'base_10_to_base_62' atom_name = base_10_to_base_62(total_atom_counter + 1); ^ src/protocols/protein_grid/ProteinGrid.cc:1117:16: error: use of undeclared identifier 'base_10_to_base_62' atom_name = base_10_to_base_62(total_atom_counter + 2); ^ src/protocols/protein_grid/ProteinGrid.cc:1136:16: error: use of undeclared identifier 'base_10_to_base_62' atom_name = base_10_to_base_62(total_atom_counter + 1); ^ src/protocols/protein_grid/ProteinGrid.cc:1160:3: error: unknown type name 'ResidueTypeCOP'; did you mean 'core::chemical::ResidueTypeCOP'? ResidueTypeCOP my_rt(ResidueType::make(my_mrt)); ^~~~~~~~~~~~~~ core::chemical::ResidueTypeCOP src/core/chemical/ResidueType.fwd.hh:42:61: note: 'core::chemical::ResidueTypeCOP' declared here typedef utility::pointer::shared_ptr< ResidueType const > ResidueTypeCOP; ^ src/protocols/protein_grid/ProteinGrid.cc:1160:24: error: use of undeclared identifier 'ResidueType'; did you mean 'core::chemical::ResidueType'? ResidueTypeCOP my_rt(ResidueType::make(my_mrt)); ^~~~~~~~~~~ core::chemical::ResidueType src/core/chemical/ResidueType.hh:124:7: note: 'core::chemical::ResidueType' declared here class ResidueType : public ResidueTypeBase, public utility::pointer::enable_shared_from_this< ResidueType > ^ src/protocols/protein_grid/ProteinGrid.cc:1163:61: error: no member named 'ResidueFactory' in namespace 'core::conformation' core::conformation::ResidueOP my_res( core::conformation::ResidueFactory::create_residue(*my_rt)); ~~~~~~~~~~~~~~~~~~~~^ src/protocols/protein_grid/ProteinGrid.cc:1163:39: error: parentheses were disambiguated as a function declaration [-Werror,-Wvexing-parse] core::conformation::ResidueOP my_res( core::conformation::ResidueFactory::create_residue(*my_rt)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/protocols/protein_grid/ProteinGrid.cc:1163:41: note: add a pair of parentheses to declare a variable core::conformation::ResidueOP my_res( core::conformation::ResidueFactory::create_residue(*my_rt)); ^ ( src/protocols/protein_grid/ProteinGrid.cc:1206:27: error: out-of-line definition of 'base_10_to_base_62' does not match any declaration in 'protocols::protein_grid::ProteinGrid' std::string ProteinGrid::base_10_to_base_62(core::Size starting_num) ^~~~~~~~~~~~~~~~~~ 14 errors generated. clang++ -o build/src/debug/macos/12.6/64/x86/clang/14.0/default/libnumeric.dylib -dynamiclib -install_name /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/src/debug/macos/12.6/64/x86/clang/14.0/default/libnumeric.dylib -stdlib=libc++ build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/agglomerative_hierarchical_clustering.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/Calculator.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/ClusteringTreeNode.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/color_util.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/constants.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/cubic_polynomial.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/cyclic_coordinate_descent.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/DiscreteIntervalEncodingTree.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/HomogeneousTransform.srlz.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/MathMatrix.srlz.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/MathVector.srlz.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/MultiDimensionalHistogram.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/polynomial.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/prob_util.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/roc_curve.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/util.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/xyz.serialization.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/zscores.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/alignment/rmsd_calc.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/crick_equations/BundleParams.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/crick_equations/HelixParams.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/expression_parser/Arithmetic.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/fourier/FFT.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/fourier/kiss_fft.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/fourier/kiss_fft_state.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/fourier/SHT.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/geometry/BoundingBox.srlz.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/geometry/projection_area.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/geometry/ring_plane.functions.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/geometry/hashing/MinimalClashHash.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/geometry/hashing/SixDHasher.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/geometry/hashing/xyzStripeHash.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/interpolation/util.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/interpolation/Histogram.srlz.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/interpolation/spline/BicubicSpline.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/interpolation/spline/CompoundInterpolator.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/interpolation/spline/CubicSpline.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/interpolation/spline/Interpolator.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/interpolation/spline/SimpleInterpolator.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/interpolation/spline/spline_functions.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/interpolation/spline/SplineGenerator.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/interpolation/spline/TricubicSpline.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/interpolation/spline/PolycubicSpline.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kdtree/calc_distance.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kdtree/construct_kdtree.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kdtree/HyperRectangle.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kdtree/KDNode.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kdtree/KDPoint.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kdtree/KDPointList.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kdtree/KDTree.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kdtree/nearest_neighbors.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kdtree/util.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kinematic_closure/bridgeObjects.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kinematic_closure/closure.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kinematic_closure/dixon.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kinematic_closure/kinematic_closure_helpers.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kinematic_closure/sturm.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kinematic_closure/vector.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/kinematic_closure/bridgeObjects_nonredundant.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/linear_algebra/rgg.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/linear_algebra/singular_value_decomposition.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/linear_algebra/EllipseParameters.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/linear_algebra/minimum_bounding_ellipse.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/model_quality/functions.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/model_quality/maxsub.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/model_quality/rms.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/model_quality/RmsData.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/nls/lmmin.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/random/random.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/random/random_xyz.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/random/WeightedSampler.os build/src/debug/macos/12.6/64/x86/clang/14.0/default/numeric/statistics/functions.os -Lexternal/lib -Lbuild/src/debug/macos/12.6/64/x86/clang/14.0/default -Lsrc -Lbuild/external/debug/macos/12.6/64/x86/clang/14.0/default -Lexternal -L/usr/lib -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes scons: *** [build/src/debug/macos/12.6/64/x86/clang/14.0/default/protocols/protein_grid/ProteinGrid.os] Error 1 scons: building terminated because of errors.
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