Test: ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20561」
Test files: 「file-system-view」 「file-list-view」
Daemon: hojo-3     Started at: 2024-10-11 12:55:41     Run time: 1:30:02      State: build failed


Test Log

Building PyRosetta MinSizeRel... Command line: cd /home/benchmark/rosetta/source/src/python/PyRosetta && /home/benchmark/prefix/hojo-3/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/bin/python3.8 build.py -j16 --compiler clang --type MinSizeRel --python-include-dir=/home/benchmark/prefix/hojo-3/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8 --python-lib=/home/benchmark/prefix/hojo-3/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 37 24.1M 37 9263k 0 0 6022k 0 0:00:04 0:00:01 0:00:03 6019k 74 24.1M 74 17.8M 0 0 7277k 0 0:00:03 0:00:02 0:00:01 7274k 100 24.1M 100 24.1M 0 0 7303k 0 0:00:03 0:00:03 --:--:-- 7303k 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 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 79 11.3M 79 9271k 0 0 8624k 0 0:00:01 0:00:01 --:--:-- 8616k 100 11.3M 100 11.3M 0 0 6920k 0 0:00:01 0:00:01 --:--:-- 6916k 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 -j16 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... [5090/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/DomainAssembly.cc.o [5091/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/FoldConstraints.cc.o [5092/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/PairingStatistics.cc.o [5093/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/StrandConstraints.cc.o [5094/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/ClassicAbinitio.cc.o [5095/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/Protocol.cc.o [5096/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/ConstraintPreparer.cc.o [5097/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/LoopJumpFoldCst.cc.o [5098/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/TemplateJumpSetup.cc.o [5099/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/ResolutionSwitcher.cc.o [5100/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/Template.cc.o [5101/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/FragmentCM.cc.o [5102/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/JumpSampleData.cc.o [5103/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/AbrelaxApplication.cc.o [5104/8715] Building CXX object 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/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/IdentifyLigandMotifs.cc.o -MF CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc.o.d -o CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc.o -c /home/benchmark/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc /home/benchmark/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc:778:31: error: expected ';' in 'for' statement specifier for ( auto sig_res_pos = 1 : mandatory_residues_for_motifs ){ ^ /home/benchmark/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc:778:31: error: expected expression 2 errors generated. [5193/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/DistanceScoreMover.cc.o [5194/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/MotifDnaPacker.cc.o [5195/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakCalibrator.cc.o [5196/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/CrossPeakList.cc.o [5197/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakAssignmentResidueMap.cc.o [5198/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/MotifSearch.cc.o [5199/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakAssignment.cc.o [5200/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/FragmentExtension.cc.o [5201/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandMotifSearch.cc.o [5202/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o [5203/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakFileFormat.cc.o [5204/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/motif_utils.cc.o [5205/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakAssignmentParameters.cc.o [5206/8715] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/NoesyModule.cc.o [5207/8715] 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

{}