Test: ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20708」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-2     Started at: 2025-04-02 16:33:22     Run time: 0:54:24      State: build failed


Test Log

Building PyRosetta MinSizeRel... Command line: cd /home/benchmark/rosetta/source/src/python/PyRosetta && /home/benchmark/prefix/nobu-2/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/bin/python3.8 build.py -j32 --compiler clang --type MinSizeRel --python-include-dir=/home/benchmark/prefix/nobu-2/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8 --python-lib=/home/benchmark/prefix/nobu-2/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/lib --multi-threaded --serialization Creating PyRosetta in "MinSizeRel" mode in: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread Getting main repository root... cd /home/benchmark/rosetta/source && git rev-parse --show-toplevel /home/benchmark/rosetta Updating Pybind11 Git submodule... cd /home/benchmark/rosetta/source/.. && git submodule update --init -- source/external/pybind11 Updating Binder Git submodule... cd /home/benchmark/rosetta/source/.. && git submodule update --init -- source/src/python/PyRosetta/binder LLVM build detected, but config/binder version has changed, perfoming a clean rebuild... Download LLVM source... cd /home/benchmark/rosetta/source/build/prefix && mkdir llvm-6.0.1.src && curl -LJ https://releases.llvm.org/6.0.1/llvm-6.0.1.src.tar.xz | tar --strip-components=1 -Jxom -C llvm-6.0.1.src && mv llvm-6.0.1.src /home/benchmark/rosetta/source/build/prefix/llvm-6.0.1 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0 7 24.1M 7 1736k 0 0 612k 0 0:00:40 0:00:02 0:00:38 612k 49 24.1M 49 11.8M 0 0 3230k 0 0:00:07 0:00:03 0:00:04 3229k 70 24.1M 70 16.9M 0 0 3553k 0 0:00:06 0:00:04 0:00:02 3553k 100 24.1M 100 24.1M 0 0 4325k 0 0:00:05 0:00:05 --:--:-- 5878k Download Clang source... cd /home/benchmark/rosetta/source/build/prefix && mkdir clang-6.0.1.src && curl -LJ https://releases.llvm.org/6.0.1/cfe-6.0.1.src.tar.xz | tar --strip-components=1 -Jxom -C clang-6.0.1.src && mv clang-6.0.1.src /home/benchmark/rosetta/source/build/prefix/llvm-6.0.1/tools/clang % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 85 11.3M 85 9887k 0 0 9907k 0 0:00:01 --:--:-- 0:00:01 9897k 100 11.3M 100 11.3M 0 0 9176k 0 0:00:01 0:00:01 --:--:-- 9176k Building tool: binder... cd /home/benchmark/rosetta/source/build/prefix/llvm-6.0.1/llvm-6.0.1.Linux-5.4.0-84-generic-x86_64-with-glibc2.27.release && cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DCMAKE_C_COMPILER=`which clang` -DCMAKE_CXX_COMPILER=`which clang++` -DLLVM_ENABLE_EH=1 -DLLVM_ENABLE_RTTI=ON .. && ninja binder tools/clang/lib/Headers/clang-headers -j32 Updating compilation submodules, version, options and residue-type-enum files... cd /home/benchmark/rosetta/source && ./update_submodules.sh PyRosetta bcl zeromq && ./version.py && ./update_options.sh && ./update_ResidueType_enum_files.sh Updating submodules needed for compilation. ...truncated... [4833/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/fold_from_loops/utils/utils.cc.o [4834/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/jumping/DisulfPairingLibrary.cc.o [4835/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/jumping/ResiduePairJump.cc.o [4836/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/hybridization/HybridizeFoldtreeDynamic.cc.o [4837/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/jumping/JumpSetup.cc.o [4838/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/hybridization/DomainAssembly.cc.o [4839/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/hybridization/TMalign.cc.o [4840/8253] Building CXX object 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CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/DensSkeleton.cc.o [4848/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/AbrelaxApplication.cc.o [4849/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/hybridization/util.cc.o [4850/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/loop_build/LoopmodelWrapper.cc.o [4851/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/hybridization/MRMover.cc.o [4852/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/CovalentCompliance.cc.o [4853/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/jumping/MembraneJump.cc.o [4854/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/jumping/PairingLibrary.cc.o [4855/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/BuildPosition.cc.o [4856/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/util.cc.o [4857/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/jumping/ResiduePairJumpSetup.cc.o [4858/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/CrossPeakInfo.cc.o [4859/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/hybridization/CartesianSampler.cc.o [4860/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/SingleMotif.cc.o [4861/8253] Building CXX object 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CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/Resonance.cc.o [4876/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/SheetSampler.cc.o [4877/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/Motif.cc.o [4878/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/StructureIndependentPeakCalibrator.cc.o [4879/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/jumping/JumpSample.cc.o [4880/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/IterativeBase.cc.o [4881/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/IRCollection.cc.o [4882/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/CrossPeak.cc.o [4883/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakAssignment.cc.o [4884/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakAssignmentResidueMap.cc.o [4885/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/StructureDependentPeakCalibrator.cc.o [4886/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/FragsToAtomDist.cc.o [4887/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o FAILED: CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o /usr/bin/clang++ -DBCL_NO_OS_SIGNAL_HANDLING -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_SYSTEM_NO_DEPRECATED -DMULTI_THREADED -DNDEBUG -DNOCRASHREPORT -DPTR_STD -DPYROSETTA -DSERIALIZATION -I/home/benchmark/prefix/nobu-2/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8 -isystem /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/external -isystem /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/external/include -isystem /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/external/boost_submod -isystem /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/external/dbio -isystem /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/external/dbio/sqlite3 -isystem /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/external/libxml2/include -isystem /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/external/rdkit -isystem /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/external/bcl/include -isystem /home/benchmark/rosetta/source/external/pybind11/include -I/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/src -I/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/src/platform/linux -std=c++11 -fvisibility=hidden -fvisibility-inlines-hidden -Os -DNDEBUG -fPIC -Werror=non-virtual-dtor -MD -MT CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o -MF CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o.d -o CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o -c /home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc /home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:757:6: error: type 'protocols::protein_grid::ProteinGridOP' (aka 'shared_ptr<protocols::protein_grid::ProteinGrid>') does not provide a call operator clash_pose_grid_(new protocols::protein_grid::ProteinGrid(working_pose_, resolution_increase_factor)); ^~~~~~~~~~~~~~~~ /home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:772:27: error: no matching constructor for initialization of 'protocols::protein_grid::ProteinGrid' clash_pose_grid_(new protocols::protein_grid::ProteinGrid(working_pose_, resolution_increase_factor, binding_pocket_center_xyz, binding_pocket_dimensions)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/src/protocols/protein_grid/ProteinGrid.hh:62:2: note: candidate constructor not viable: no known conversion from 'utility::vector1<core::Size>' (aka 'vector1<unsigned long>') to 'numeric::xyzVector<int>' for 3rd argument ProteinGrid(core::pose::PoseOP in_pose, core::Real resolution, numeric::xyzVector<int> sub_area_center, utility::vector1<core::Size> sub_region_dimensions); ^ /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/src/protocols/protein_grid/ProteinGrid.hh:59:2: note: candidate constructor not viable: requires 3 arguments, but 4 were provided ProteinGrid(core::pose::PoseOP in_pose, numeric::xyzVector<int> sub_area_center, utility::vector1<core::Size> sub_region_dimensions); ^ /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/src/protocols/protein_grid/ProteinGrid.hh:56:2: note: candidate constructor not viable: requires 2 arguments, but 4 were provided ProteinGrid(core::pose::PoseOP in_pose, core::Real resolution); ^ /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/src/protocols/protein_grid/ProteinGrid.hh:53:2: note: candidate constructor not viable: requires single argument 'in_pose', but 4 arguments were provided ProteinGrid(core::pose::PoseOP in_pose); ^ /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/src/protocols/protein_grid/ProteinGrid.hh:65:2: note: candidate constructor not viable: requires single argument 'other', but 4 arguments were provided ProteinGrid( ProteinGrid const & other ); ^ /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/src/protocols/protein_grid/ProteinGrid.hh:137:2: note: candidate constructor not viable: requires 0 arguments, but 4 were provided ProteinGrid(); ^ /home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:775:4: error: expected expression else ^ /home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:784:4: error: type 'protocols::protein_grid::ProteinGridOP' (aka 'shared_ptr<protocols::protein_grid::ProteinGrid>') does not provide a call operator clash_pose_grid_(new protocols::protein_grid::ProteinGrid(working_pose_, resolution_increase_factor)); ^~~~~~~~~~~~~~~~ /home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:788:3: error: type 'protocols::protein_grid::ProteinGridOP' (aka 'shared_ptr<protocols::protein_grid::ProteinGrid>') does not provide a call operator sf_pose_grid_(new protocols::protein_grid::ProteinGrid(*clash_pose_grid_)); ^~~~~~~~~~~~~ /home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:983:7: error: type 'protocols::protein_grid::ProteinGridOP' (aka 'shared_ptr<protocols::protein_grid::ProteinGrid>') does not provide a call operator working_sf_pose_grid(new protocols::protein_grid::ProteinGrid(*sf_pose_grid_)); ^~~~~~~~~~~~~~~~~~~~ 6 errors generated. [4888/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc.o [4889/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/hybridization/HybridizeProtocol.cc.o [4890/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegment.cc.o [4891/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/ResonanceList.cc.o [4892/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/CrossPeakList.cc.o [4893/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/hybridization/FoldTreeHybridize.cc.o [4894/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakFileFormat.cc.o [4895/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/motif_utils.cc.o [4896/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakAssignmentParameters.cc.o [4897/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/ProteinMPNNMover.cc.o [4898/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/MotifSearch.cc.o [4899/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc.o [4900/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/MakeStarTopology.cc.o [4901/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/NoesyModule.cc.o [4902/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/CentroidRelaxMover.cc.o [4903/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/AutoRBRelaxMover.cc.o [4904/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/FragmentExtension.cc.o [4905/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/MotifDnaPacker.cc.o [4906/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegmentRelax_main.cc.o [4907/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/IdealizeHelices.cc.o [4908/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegmentMover.cc.o [4909/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegmentRelax.cc.o [4910/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandMotifSearch.cc.o [4911/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/FragInsertAndAlignMover.cc.o [4912/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/FullatomRelaxMover.cc.o [4913/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/ProteinMPNNProbabilitiesMetric.cc.o [4914/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/OptimizeThreading.cc.o [4915/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/util.cc.o [4916/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/SurfaceDockingProtocol.cc.o [4917/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/ConfChangeMover.cc.o [4918/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/LoopGrower.cc.o ninja: build stopped: subcommand failed.

Sub-Tests Results

All sub-tests

JSON output

{}