Test: mac.clang.build.ninja_graphics 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20477」
Test files: 「file-system-view」 「file-list-view」
Daemon: hikaru-2     Started at: 2024-09-17 17:32:49     Run time: 0:10:14      State: failed


Test Log

Running: ./ninja_build.py graphics -v -remake -j32 ['z', 'zlib', 'cppdb', 'sqlite3', 'cifparse', 'libxml2', 'libzmq', 'rdkit', 'bcl', 'cmaes'] Running versioning script ... Done. (0.2 seconds) Number of option files updated: 0 Total 4708 options. Updating submodules needed for compilation. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed Examining external z Examining external zlib making external project files for project zlib ...done. Examining external cppdb Examining external sqlite3 Examining external cifparse making external project files for project cifparse ...done. Examining external libxml2 making external project files for project libxml2 ...done. Examining external libzmq making external project files for project libzmq ...done. Examining external rdkit making external project files for project rdkit ...done. Examining external bcl making external project files for project bcl ...done. Examining external cmaes making external project files for project cmaes ...done. making project files for project ObjexxFCL ...done. making project files for project utility ...done. making project files for project numeric ...done. making project files for project basic ...done. making project files for project core.1 ...done. making project files for project core.2 ...done. making project files for project core.3 ...done. making project files for project core.4 ...done. making project files for project core.5 ...done. making project files for project core.6 ...done. making project files for project protocols.1 ...done. making project files for project protocols_a.2 ...done. making project files for project protocols_b.2 ...done. making project files for project protocols.3 ...done. making project files for project protocols.4 ...done. making project files for project protocols_a.5 ...done. making project files for project protocols_b.5 ...done. making project files for project protocols_c.5 ...done. making project files for project protocols_d.5 ...done. making project files for project protocols_e.5 ...done. making project files for project protocols_f.5 ...done. making project files for project protocols_g.5 ...done. making project files for project protocols_h.5 ...done. making project files for project protocols_a.6 ...done. making project files for project protocols_b.6 ...done. making project files for project protocols_c.6 ...done. making project files for project protocols_d.6 ...done. making project files for project protocols_e.6 ...done. making project files for project protocols.7 ...done. making project files for project protocols.8 ...done. making project files for project devel ...done. making project files for project apps ...done. Found /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/pilot_apps.src.settings.all and going to use it! making project files for project pilot_apps ...done. making test files for test numeric ...done. making test files for test utility ...done. making test files for test ObjexxFCL ...done. making test files for test basic ...done. making test files for test core ...done. making test files for test protocols ...done. making test files for test apps ...done. making test files for test devel ...done. CMake Warning: No source or binary directory provided. Both will be assumed to be the same as the current working directory, but note that this warning will become a fatal error in future CMake releases.  CMake Warning (dev) in CMakeLists.txt: No project() command is present. The top-level CMakeLists.txt file must contain a literal, direct call to the project() command. Add a line of code such as project(ProjectName) near the top of the file, but after cmake_minimum_required(). CMake is pretending there is a "project(Project)" command on the first line. This warning is for project developers. Use -Wno-dev to suppress it.  CMake Deprecation Warning at CMakeLists.txt:1 (CMAKE_MINIMUM_REQUIRED): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument <min> value or use a ...<max> suffix to tell CMake that the project does not need compatibility with older versions.  >> CMAKE identifies C++ compiler as 'Clang', interpreting this as 'clang' >> To change, set CXX and CC environment variables (or pass -DCMAKE_CXX_COMPILER) and do a clean rebuild. >> current settings: CXX='' CC='' -- Compiler: clang Updating submodules needed for compilation. -- Configuring done -- Generating done -- Build files have been written to: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics ninja: Entering directory `/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics' [1/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/oop_creator ../../bin/oop_creator && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/oop_creator ../../bin/oop_creator.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/oop_creator ../../bin/oop_creator.default.macosclangrelease [2/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/r_broker ../../bin/r_broker && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/r_broker ../../bin/r_broker.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/r_broker ../../bin/r_broker.default.macosclangrelease [3/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/burial_measure_centroid ../../bin/burial_measure_centroid && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/burial_measure_centroid ../../bin/burial_measure_centroid.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/burial_measure_centroid ../../bin/burial_measure_centroid.default.macosclangrelease [4/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/features_database_schema ../../bin/features_database_schema && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/features_database_schema ../../bin/features_database_schema.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/features_database_schema ../../bin/features_database_schema.default.macosclangrelease [5/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/load_membrane_pose ../../bin/load_membrane_pose && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/load_membrane_pose ../../bin/load_membrane_pose.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/load_membrane_pose ../../bin/load_membrane_pose.default.macosclangrelease [6/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/format_converter ../../bin/format_converter && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/format_converter ../../bin/format_converter.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/format_converter ../../bin/format_converter.default.macosclangrelease [7/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/oop_dock_design ../../bin/oop_dock_design && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/oop_dock_design ../../bin/oop_dock_design.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/oop_dock_design ../../bin/oop_dock_design.default.macosclangrelease [8/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/glycomutagenesis ../../bin/glycomutagenesis && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/glycomutagenesis ../../bin/glycomutagenesis.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/glycomutagenesis ../../bin/glycomutagenesis.default.macosclangrelease [9/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/loophash_createdb ../../bin/loophash_createdb && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/loophash_createdb ../../bin/loophash_createdb.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/loophash_createdb ../../bin/loophash_createdb.default.macosclangrelease [10/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/silent2frag ../../bin/silent2frag && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/silent2frag ../../bin/silent2frag.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/silent2frag ../../bin/silent2frag.default.macosclangrelease [11/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/r_pdb2top ../../bin/r_pdb2top && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/r_pdb2top ../../bin/r_pdb2top.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/r_pdb2top ../../bin/r_pdb2top.default.macosclangrelease [12/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/ld_converter ../../bin/ld_converter && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/ld_converter ../../bin/ld_converter.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/ld_converter ../../bin/ld_converter.default.macosclangrelease [13/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/batchrelax ../../bin/batchrelax && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/batchrelax ../../bin/batchrelax.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/batchrelax ../../bin/batchrelax.default.macosclangrelease [14/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/crossaln ../../bin/crossaln && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/crossaln ../../bin/crossaln.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/crossaln ../../bin/crossaln.default.macosclangrelease [15/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cloud_app ../../bin/cloud_app && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cloud_app ../../bin/cloud_app.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cloud_app ../../bin/cloud_app.default.macosclangrelease [16/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cmaes_minimizer_test ../../bin/cmaes_minimizer_test && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cmaes_minimizer_test ../../bin/cmaes_minimizer_test.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cmaes_minimizer_test ../../bin/cmaes_minimizer_test.default.macosclangrelease [17/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/inv_kin_lig_loop_design ../../bin/inv_kin_lig_loop_design && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/inv_kin_lig_loop_design ../../bin/inv_kin_lig_loop_design.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/inv_kin_lig_loop_design ../../bin/inv_kin_lig_loop_design.default.macosclangrelease [18/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/design_glycans ../../bin/design_glycans && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/design_glycans ../../bin/design_glycans.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/design_glycans ../../bin/design_glycans.default.macosclangrelease [19/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/RescorePDDF ../../bin/RescorePDDF && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/RescorePDDF ../../bin/RescorePDDF.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/RescorePDDF ../../bin/RescorePDDF.default.macosclangrelease [20/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_manager_multirun_test ../../bin/tensorflow_manager_multirun_test && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_manager_multirun_test ../../bin/tensorflow_manager_multirun_test.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_manager_multirun_test ../../bin/tensorflow_manager_multirun_test.default.macosclangrelease [21/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/angle_recovery_stats ../../bin/angle_recovery_stats && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/angle_recovery_stats ../../bin/angle_recovery_stats.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/angle_recovery_stats ../../bin/angle_recovery_stats.default.macosclangrelease [22/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hbonds_test ../../bin/hbonds_test && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hbonds_test ../../bin/hbonds_test.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hbonds_test ../../bin/hbonds_test.default.macosclangrelease [23/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/Cyclize ../../bin/Cyclize && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/Cyclize ../../bin/Cyclize.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/Cyclize ../../bin/Cyclize.default.macosclangrelease [24/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/RescoreSAXS ../../bin/RescoreSAXS && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/RescoreSAXS ../../bin/RescoreSAXS.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/RescoreSAXS ../../bin/RescoreSAXS.default.macosclangrelease [25/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/number_of_residuetypes ../../bin/number_of_residuetypes && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/number_of_residuetypes ../../bin/number_of_residuetypes.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/number_of_residuetypes ../../bin/number_of_residuetypes.default.macosclangrelease [26/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_manager_multi_input_test ../../bin/tensorflow_manager_multi_input_test && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_manager_multi_input_test ../../bin/tensorflow_manager_multi_input_test.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_manager_multi_input_test ../../bin/tensorflow_manager_multi_input_test.default.macosclangrelease [27/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_manager_test1 ../../bin/tensorflow_manager_test1 && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_manager_test1 ../../bin/tensorflow_manager_test1.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_manager_test1 ../../bin/tensorflow_manager_test1.default.macosclangrelease [28/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_test2 ../../bin/tensorflow_test2 && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_test2 ../../bin/tensorflow_test2.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_test2 ../../bin/tensorflow_test2.default.macosclangrelease [29/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_rosetta_thread_manager_preallocation ../../bin/test_rosetta_thread_manager_preallocation && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_rosetta_thread_manager_preallocation ../../bin/test_rosetta_thread_manager_preallocation.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_rosetta_thread_manager_preallocation ../../bin/test_rosetta_thread_manager_preallocation.default.macosclangrelease [30/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/loophash.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/pilot/mike/loophash.cc.o -o loophash -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [31/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/test1.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/pilot/phil/test1.cc.o -o test1 -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [32/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/r_rmsf.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/pilot/olli/r_rmsf.cc.o -o r_rmsf -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [33/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/assemble_domains_jd2 ../../bin/assemble_domains_jd2 && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/assemble_domains_jd2 ../../bin/assemble_domains_jd2.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/assemble_domains_jd2 ../../bin/assemble_domains_jd2.default.macosclangrelease [34/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/jrelax ../../bin/jrelax && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/jrelax ../../bin/jrelax.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/jrelax ../../bin/jrelax.default.macosclangrelease [35/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/jscore ../../bin/jscore && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/jscore ../../bin/jscore.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/jscore ../../bin/jscore.default.macosclangrelease [36/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hotspot_hash ../../bin/hotspot_hash && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hotspot_hash ../../bin/hotspot_hash.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hotspot_hash ../../bin/hotspot_hash.default.macosclangrelease [37/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mp_find_interface ../../bin/mp_find_interface && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mp_find_interface ../../bin/mp_find_interface.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mp_find_interface ../../bin/mp_find_interface.default.macosclangrelease [38/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hshash_utils ../../bin/hshash_utils && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hshash_utils ../../bin/hshash_utils.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hshash_utils ../../bin/hshash_utils.default.macosclangrelease [39/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mpdocking_setup ../../bin/mpdocking_setup && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mpdocking_setup ../../bin/mpdocking_setup.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mpdocking_setup ../../bin/mpdocking_setup.default.macosclangrelease [40/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/jd2test ../../bin/jd2test && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/jd2test ../../bin/jd2test.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/jd2test ../../bin/jd2test.default.macosclangrelease [41/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/interface_statistics ../../bin/interface_statistics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/interface_statistics ../../bin/interface_statistics.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/interface_statistics ../../bin/interface_statistics.default.macosclangrelease [42/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mp_quick_relax ../../bin/mp_quick_relax && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mp_quick_relax ../../bin/mp_quick_relax.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mp_quick_relax ../../bin/mp_quick_relax.default.macosclangrelease [43/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/per_residue_sc_sasa ../../bin/per_residue_sc_sasa && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/per_residue_sc_sasa ../../bin/per_residue_sc_sasa.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/per_residue_sc_sasa ../../bin/per_residue_sc_sasa.default.macosclangrelease [44/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_CCD_loop_closure ../../bin/test_CCD_loop_closure && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_CCD_loop_closure ../../bin/test_CCD_loop_closure.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_CCD_loop_closure ../../bin/test_CCD_loop_closure.default.macosclangrelease [45/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/range_relax ../../bin/range_relax && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/range_relax ../../bin/range_relax.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/range_relax ../../bin/range_relax.default.macosclangrelease [46/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_CarbohydrateInfo ../../bin/test_CarbohydrateInfo && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_CarbohydrateInfo ../../bin/test_CarbohydrateInfo.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_CarbohydrateInfo ../../bin/test_CarbohydrateInfo.default.macosclangrelease [47/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_EnergyMethodOptions ../../bin/test_EnergyMethodOptions && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_EnergyMethodOptions ../../bin/test_EnergyMethodOptions.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_EnergyMethodOptions ../../bin/test_EnergyMethodOptions.default.macosclangrelease [48/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_RingConformationMover ../../bin/test_RingConformationMover && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_RingConformationMover ../../bin/test_RingConformationMover.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_RingConformationMover ../../bin/test_RingConformationMover.default.macosclangrelease [49/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_SiteConstraint ../../bin/test_SiteConstraint && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_SiteConstraint ../../bin/test_SiteConstraint.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_SiteConstraint ../../bin/test_SiteConstraint.default.macosclangrelease [50/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_carbohydrate_scoring ../../bin/test_carbohydrate_scoring && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_carbohydrate_scoring ../../bin/test_carbohydrate_scoring.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_carbohydrate_scoring ../../bin/test_carbohydrate_scoring.default.macosclangrelease [51/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_coenzymes ../../bin/test_coenzymes && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_coenzymes ../../bin/test_coenzymes.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_coenzymes ../../bin/test_coenzymes.default.macosclangrelease [52/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_explicit_membrane_input ../../bin/test_explicit_membrane_input && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_explicit_membrane_input ../../bin/test_explicit_membrane_input.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_explicit_membrane_input ../../bin/test_explicit_membrane_input.default.macosclangrelease [53/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_carbohydrate_docking ../../bin/test_carbohydrate_docking && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_carbohydrate_docking ../../bin/test_carbohydrate_docking.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_carbohydrate_docking ../../bin/test_carbohydrate_docking.default.macosclangrelease [54/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_non-canonical_connectivities ../../bin/test_non-canonical_connectivities && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_non-canonical_connectivities ../../bin/test_non-canonical_connectivities.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_non-canonical_connectivities ../../bin/test_non-canonical_connectivities.default.macosclangrelease [55/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/enumerate_rotamers ../../bin/enumerate_rotamers && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/enumerate_rotamers ../../bin/enumerate_rotamers.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/enumerate_rotamers ../../bin/enumerate_rotamers.default.macosclangrelease [56/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/version_mpscorefxn ../../bin/version_mpscorefxn && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/version_mpscorefxn ../../bin/version_mpscorefxn.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/version_mpscorefxn ../../bin/version_mpscorefxn.default.macosclangrelease [57/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rb_entropy ../../bin/rb_entropy && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rb_entropy ../../bin/rb_entropy.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rb_entropy ../../bin/rb_entropy.default.macosclangrelease [58/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/read_tensor ../../bin/read_tensor && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/read_tensor ../../bin/read_tensor.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/read_tensor ../../bin/read_tensor.default.macosclangrelease [59/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/color_by_lipid_type ../../bin/color_by_lipid_type && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/color_by_lipid_type ../../bin/color_by_lipid_type.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/color_by_lipid_type ../../bin/color_by_lipid_type.default.macosclangrelease [60/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/screen_phosphates ../../bin/screen_phosphates && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/screen_phosphates ../../bin/screen_phosphates.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/screen_phosphates ../../bin/screen_phosphates.default.macosclangrelease [61/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hotspot_stub_constraint_test ../../bin/hotspot_stub_constraint_test && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hotspot_stub_constraint_test ../../bin/hotspot_stub_constraint_test.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hotspot_stub_constraint_test ../../bin/hotspot_stub_constraint_test.default.macosclangrelease [62/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/loophash ../../bin/loophash && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/loophash ../../bin/loophash.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/loophash ../../bin/loophash.default.macosclangrelease [63/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test1 ../../bin/test1 && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test1 ../../bin/test1.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test1 ../../bin/test1.default.macosclangrelease [64/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/r_rmsf ../../bin/r_rmsf && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/r_rmsf ../../bin/r_rmsf.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/r_rmsf ../../bin/r_rmsf.default.macosclangrelease [65/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/PDB_diagnostic ../../bin/PDB_diagnostic && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/PDB_diagnostic ../../bin/PDB_diagnostic.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/PDB_diagnostic ../../bin/PDB_diagnostic.default.macosclangrelease [66/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/LoopAnalyzer ../../bin/LoopAnalyzer && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/LoopAnalyzer ../../bin/LoopAnalyzer.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/LoopAnalyzer ../../bin/LoopAnalyzer.default.macosclangrelease [67/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/motif_dna_packer_design ../../bin/motif_dna_packer_design && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/motif_dna_packer_design ../../bin/motif_dna_packer_design.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/motif_dna_packer_design ../../bin/motif_dna_packer_design.default.macosclangrelease [68/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/min_pack_min ../../bin/min_pack_min && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/min_pack_min ../../bin/min_pack_min.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/min_pack_min ../../bin/min_pack_min.default.macosclangrelease [69/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/sym_multicomp_test ../../bin/sym_multicomp_test && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/sym_multicomp_test ../../bin/sym_multicomp_test.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/sym_multicomp_test ../../bin/sym_multicomp_test.default.macosclangrelease [70/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/make_mainchain_potential ../../bin/make_mainchain_potential && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/make_mainchain_potential ../../bin/make_mainchain_potential.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/make_mainchain_potential ../../bin/make_mainchain_potential.default.macosclangrelease [71/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_test1 ../../bin/tensorflow_test1 && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_test1 ../../bin/tensorflow_test1.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/tensorflow_test1 ../../bin/tensorflow_test1.default.macosclangrelease [72/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_multithreaded_ig_correctness ../../bin/test_multithreaded_ig_correctness && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_multithreaded_ig_correctness ../../bin/test_multithreaded_ig_correctness.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_multithreaded_ig_correctness ../../bin/test_multithreaded_ig_correctness.default.macosclangrelease [73/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_rosetta_thread_manager_advanced_API ../../bin/test_rosetta_thread_manager_advanced_API && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_rosetta_thread_manager_advanced_API ../../bin/test_rosetta_thread_manager_advanced_API.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_rosetta_thread_manager_advanced_API ../../bin/test_rosetta_thread_manager_advanced_API.default.macosclangrelease [74/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/FiberDiffractionTest ../../bin/FiberDiffractionTest && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/FiberDiffractionTest ../../bin/FiberDiffractionTest.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/FiberDiffractionTest ../../bin/FiberDiffractionTest.default.macosclangrelease [75/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/fit_helixparams ../../bin/fit_helixparams && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/fit_helixparams ../../bin/fit_helixparams.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/fit_helixparams ../../bin/fit_helixparams.default.macosclangrelease [76/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mucintypeglycosylation ../../bin/mucintypeglycosylation && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mucintypeglycosylation ../../bin/mucintypeglycosylation.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mucintypeglycosylation ../../bin/mucintypeglycosylation.default.macosclangrelease [77/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_trRosettaConstraintGenerator ../../bin/test_trRosettaConstraintGenerator && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_trRosettaConstraintGenerator ../../bin/test_trRosettaConstraintGenerator.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_trRosettaConstraintGenerator ../../bin/test_trRosettaConstraintGenerator.default.macosclangrelease [78/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_rosetta_thread_manager_basic_API ../../bin/test_rosetta_thread_manager_basic_API && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_rosetta_thread_manager_basic_API ../../bin/test_rosetta_thread_manager_basic_API.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_rosetta_thread_manager_basic_API ../../bin/test_rosetta_thread_manager_basic_API.default.macosclangrelease [79/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_trRosetta ../../bin/test_trRosetta && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_trRosetta ../../bin/test_trRosetta.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_trRosetta ../../bin/test_trRosetta.default.macosclangrelease [80/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_tensorflow_graph_convolutional_nn ../../bin/test_tensorflow_graph_convolutional_nn && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_tensorflow_graph_convolutional_nn ../../bin/test_tensorflow_graph_convolutional_nn.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_tensorflow_graph_convolutional_nn ../../bin/test_tensorflow_graph_convolutional_nn.default.macosclangrelease [81/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_trRosettaProtocolMover ../../bin/test_trRosettaProtocolMover && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_trRosettaProtocolMover ../../bin/test_trRosettaProtocolMover.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_trRosettaProtocolMover ../../bin/test_trRosettaProtocolMover.default.macosclangrelease [82/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_C-terminal_conjugation ../../bin/test_C-terminal_conjugation && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_C-terminal_conjugation ../../bin/test_C-terminal_conjugation.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/test_C-terminal_conjugation ../../bin/test_C-terminal_conjugation.default.macosclangrelease [83/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/minirosetta.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/boinc/minirosetta.cc.o -o minirosetta -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [84/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/minirosetta ../../bin/minirosetta && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/minirosetta ../../bin/minirosetta.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/minirosetta ../../bin/minirosetta.default.macosclangrelease [85/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/minirosetta_graphics.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/boinc/minirosetta_graphics.cc.o -MF CMakeFiles/minirosetta_graphics.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/boinc/minirosetta_graphics.cc.o.d -o CMakeFiles/minirosetta_graphics.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/boinc/minirosetta_graphics.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/boinc/minirosetta_graphics.cc [86/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/minirosetta_graphics.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/boinc/minirosetta_graphics.cc.o -o minirosetta_graphics -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [87/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/minirosetta_graphics ../../bin/minirosetta_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/minirosetta_graphics ../../bin/minirosetta_graphics.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/minirosetta_graphics ../../bin/minirosetta_graphics.default.macosclangrelease [88/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/GlycanDock.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/GlycanDock.cc.o -MF CMakeFiles/GlycanDock.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/GlycanDock.cc.o.d -o CMakeFiles/GlycanDock.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/GlycanDock.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/GlycanDock.cc [89/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/GlycanDock.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/GlycanDock.cc.o -o GlycanDock -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) [90/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/GlycanDock ../../bin/GlycanDock && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/GlycanDock ../../bin/GlycanDock.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/GlycanDock ../../bin/GlycanDock.default.macosclangrelease [91/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/energy_based_clustering.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/clustering/energy_based_clustering.cc.o -MF CMakeFiles/energy_based_clustering.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/clustering/energy_based_clustering.cc.o.d -o CMakeFiles/energy_based_clustering.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/clustering/energy_based_clustering.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/clustering/energy_based_clustering.cc [92/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/energy_based_clustering.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/clustering/energy_based_clustering.cc.o -o energy_based_clustering -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) [93/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/energy_based_clustering ../../bin/energy_based_clustering && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/energy_based_clustering ../../bin/energy_based_clustering.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/energy_based_clustering ../../bin/energy_based_clustering.default.macosclangrelease [94/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/cluster_alns.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/cluster_alns.cc.o -MF CMakeFiles/cluster_alns.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/cluster_alns.cc.o.d -o CMakeFiles/cluster_alns.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/cluster_alns.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/cluster_alns.cc [95/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cluster_alns.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/cluster_alns.cc.o -o cluster_alns -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [96/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cluster_alns ../../bin/cluster_alns && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cluster_alns ../../bin/cluster_alns.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cluster_alns ../../bin/cluster_alns.default.macosclangrelease [97/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" 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-DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/docking_prepack_protocol.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/docking/docking_prepack_protocol.cc.o -o docking_prepack_protocol -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib 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/Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/glycan_info ../../bin/glycan_info && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/glycan_info ../../bin/glycan_info.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/glycan_info ../../bin/glycan_info.default.macosclangrelease [102/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/docking_prepack_protocol ../../bin/docking_prepack_protocol && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/docking_prepack_protocol ../../bin/docking_prepack_protocol.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/docking_prepack_protocol ../../bin/docking_prepack_protocol.default.macosclangrelease [103/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY 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than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [105/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/docking_protocol ../../bin/docking_protocol && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/docking_protocol ../../bin/docking_protocol.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/docking_protocol ../../bin/docking_protocol.default.macosclangrelease [106/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/pose_from_saccharide_sequence.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/pose_from_saccharide_sequence.cc.o -MF CMakeFiles/pose_from_saccharide_sequence.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/pose_from_saccharide_sequence.cc.o.d -o CMakeFiles/pose_from_saccharide_sequence.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/pose_from_saccharide_sequence.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/pose_from_saccharide_sequence.cc [107/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/pose_from_saccharide_sequence.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/pose_from_saccharide_sequence.cc.o -o pose_from_saccharide_sequence -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [108/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/pose_from_saccharide_sequence ../../bin/pose_from_saccharide_sequence && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/pose_from_saccharide_sequence ../../bin/pose_from_saccharide_sequence.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/pose_from_saccharide_sequence ../../bin/pose_from_saccharide_sequence.default.macosclangrelease [109/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/create_clash-based_repack_shell.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/create_clash-based_repack_shell.cc.o -MF CMakeFiles/create_clash-based_repack_shell.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/create_clash-based_repack_shell.cc.o.d -o CMakeFiles/create_clash-based_repack_shell.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/create_clash-based_repack_shell.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/create_clash-based_repack_shell.cc [110/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/create_clash-based_repack_shell.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/create_clash-based_repack_shell.cc.o -o create_clash-based_repack_shell -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [111/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/create_clash-based_repack_shell ../../bin/create_clash-based_repack_shell && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/create_clash-based_repack_shell ../../bin/create_clash-based_repack_shell.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/create_clash-based_repack_shell ../../bin/create_clash-based_repack_shell.default.macosclangrelease [112/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem 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macOS version (12.0) than being linked (10.10) [114/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cluster ../../bin/cluster && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cluster ../../bin/cluster.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cluster 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[131/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/ddg_monomer.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ddg/ddg_monomer.cc.o -o ddg_monomer -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [132/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/fix_alignment_to_match_pdb.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/fix_alignment_to_match_pdb.cc.o -o fix_alignment_to_match_pdb -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [133/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/calibur ../../bin/calibur && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/calibur ../../bin/calibur.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/calibur ../../bin/calibur.default.macosclangrelease [134/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/glycan_clash_check ../../bin/glycan_clash_check && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/glycan_clash_check ../../bin/glycan_clash_check.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/glycan_clash_check ../../bin/glycan_clash_check.default.macosclangrelease [135/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/ddg_monomer ../../bin/ddg_monomer && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/ddg_monomer ../../bin/ddg_monomer.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/ddg_monomer ../../bin/ddg_monomer.default.macosclangrelease [136/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/fix_alignment_to_match_pdb ../../bin/fix_alignment_to_match_pdb && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/fix_alignment_to_match_pdb ../../bin/fix_alignment_to_match_pdb.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/fix_alignment_to_match_pdb ../../bin/fix_alignment_to_match_pdb.default.macosclangrelease [137/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_extract.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/rna_extract.cc.o -o rna_extract -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [138/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_features.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/rna_features.cc.o -o rna_features -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [139/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_extract ../../bin/rna_extract && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_extract ../../bin/rna_extract.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_extract ../../bin/rna_extract.default.macosclangrelease [140/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_features ../../bin/rna_features && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_features ../../bin/rna_features.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_features ../../bin/rna_features.default.macosclangrelease [141/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_graft.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/rna_graft.cc.o -o rna_graft -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [142/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_helix.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/rna_helix.cc.o -o rna_helix -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) [143/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_graft ../../bin/rna_graft && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_graft ../../bin/rna_graft.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_graft ../../bin/rna_graft.default.macosclangrelease [144/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_helix ../../bin/rna_helix && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_helix ../../bin/rna_helix.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_helix ../../bin/rna_helix.default.macosclangrelease [145/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_idealize.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/rna_idealize.cc.o -o rna_idealize -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [146/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_minimize.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/rna_minimize.cc.o -o rna_minimize -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [147/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_idealize ../../bin/rna_idealize && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_idealize ../../bin/rna_idealize.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_idealize ../../bin/rna_idealize.default.macosclangrelease [148/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_minimize ../../bin/rna_minimize && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_minimize ../../bin/rna_minimize.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_minimize ../../bin/rna_minimize.default.macosclangrelease [149/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_motif.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/rna_motif.cc.o -o rna_motif -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [150/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/dock_glycans.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/dock_glycans.cc.o -MF CMakeFiles/dock_glycans.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/dock_glycans.cc.o.d -o CMakeFiles/dock_glycans.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/dock_glycans.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/dock_glycans.cc [151/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_predict_chem_map.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/rna_predict_chem_map.cc.o -o rna_predict_chem_map -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [152/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_motif ../../bin/rna_motif && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_motif ../../bin/rna_motif.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_motif ../../bin/rna_motif.default.macosclangrelease [153/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_predict_chem_map ../../bin/rna_predict_chem_map && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_predict_chem_map ../../bin/rna_predict_chem_map.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_predict_chem_map ../../bin/rna_predict_chem_map.default.macosclangrelease [154/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/dock_glycans.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/carbohydrates/dock_glycans.cc.o -o dock_glycans -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [155/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_score.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/rna_score.cc.o -o rna_score -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) [156/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_suitename.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/rna_suitename.cc.o -o rna_suitename -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) [157/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/dock_glycans ../../bin/dock_glycans && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/dock_glycans ../../bin/dock_glycans.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/dock_glycans ../../bin/dock_glycans.default.macosclangrelease [158/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_score ../../bin/rna_score && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_score ../../bin/rna_score.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_score ../../bin/rna_score.default.macosclangrelease [159/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_suitename ../../bin/rna_suitename && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_suitename ../../bin/rna_suitename.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_suitename ../../bin/rna_suitename.default.macosclangrelease [160/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/partial_thread.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/partial_thread.cc.o -MF CMakeFiles/partial_thread.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/partial_thread.cc.o.d -o CMakeFiles/partial_thread.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/partial_thread.cc.o -c 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-DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/FiberDiffractionFreeSet.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/fiber_diffraction/FiberDiffractionFreeSet.cc.o -o FiberDiffractionFreeSet -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [163/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/BuildPeptide.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/flexpep_docking/BuildPeptide.cc.o -o BuildPeptide -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [164/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rnp_ddg ../../bin/rnp_ddg && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rnp_ddg ../../bin/rnp_ddg.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rnp_ddg ../../bin/rnp_ddg.default.macosclangrelease [165/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION 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-c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ddg/minimize_with_cst.cc [166/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names 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libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [167/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/FiberDiffractionFreeSet ../../bin/FiberDiffractionFreeSet && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/FiberDiffractionFreeSet ../../bin/FiberDiffractionFreeSet.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/FiberDiffractionFreeSet ../../bin/FiberDiffractionFreeSet.default.macosclangrelease [168/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/BuildPeptide ../../bin/BuildPeptide && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/BuildPeptide ../../bin/BuildPeptide.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/BuildPeptide ../../bin/BuildPeptide.default.macosclangrelease [169/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/partial_thread ../../bin/partial_thread && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/partial_thread ../../bin/partial_thread.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/partial_thread ../../bin/partial_thread.default.macosclangrelease [170/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/FlexPepDocking.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/flexpep_docking/FlexPepDocking.cc.o -o FlexPepDocking -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [171/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/zinc2_homodimer_setup.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc2_homodimer_setup.cc.o -MF CMakeFiles/zinc2_homodimer_setup.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc2_homodimer_setup.cc.o.d -o CMakeFiles/zinc2_homodimer_setup.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc2_homodimer_setup.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc2_homodimer_setup.cc [172/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/minimize_with_cst.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ddg/minimize_with_cst.cc.o -o minimize_with_cst -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [173/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/hydrate.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/hydrate/hydrate.cc.o -o hydrate -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [174/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/helical_bundle_predict.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/helical_bundle/helical_bundle_predict.cc.o -o helical_bundle_predict -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [175/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/FlexPepDocking ../../bin/FlexPepDocking && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/FlexPepDocking ../../bin/FlexPepDocking.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/FlexPepDocking ../../bin/FlexPepDocking.default.macosclangrelease [176/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/minimize_with_cst ../../bin/minimize_with_cst && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/minimize_with_cst ../../bin/minimize_with_cst.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/minimize_with_cst ../../bin/minimize_with_cst.default.macosclangrelease [177/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hydrate ../../bin/hydrate && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hydrate ../../bin/hydrate.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/hydrate ../../bin/hydrate.default.macosclangrelease [178/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/helical_bundle_predict ../../bin/helical_bundle_predict && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/helical_bundle_predict ../../bin/helical_bundle_predict.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/helical_bundle_predict ../../bin/helical_bundle_predict.default.macosclangrelease [179/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/zinc2_homodimer_setup.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc2_homodimer_setup.cc.o -o zinc2_homodimer_setup -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [180/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/zinc2_homodimer_setup ../../bin/zinc2_homodimer_setup && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/zinc2_homodimer_setup ../../bin/zinc2_homodimer_setup.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/zinc2_homodimer_setup ../../bin/zinc2_homodimer_setup.default.macosclangrelease [181/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/simple_cycpep_predict.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/cyclic_peptide/simple_cycpep_predict.cc.o -MF CMakeFiles/simple_cycpep_predict.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/cyclic_peptide/simple_cycpep_predict.cc.o.d -o CMakeFiles/simple_cycpep_predict.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/cyclic_peptide/simple_cycpep_predict.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/cyclic_peptide/simple_cycpep_predict.cc [182/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/supercharge.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/supercharge.cc.o -MF 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(10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [184/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/zinc2_homodimer_design.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc2_homodimer_design.cc.o -MF CMakeFiles/zinc2_homodimer_design.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc2_homodimer_design.cc.o.d -o CMakeFiles/zinc2_homodimer_design.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc2_homodimer_design.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc2_homodimer_design.cc [185/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/supercharge.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/supercharge.cc.o -o supercharge -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [186/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/simple_cycpep_predict ../../bin/simple_cycpep_predict && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/simple_cycpep_predict ../../bin/simple_cycpep_predict.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/simple_cycpep_predict ../../bin/simple_cycpep_predict.default.macosclangrelease [187/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/avrg_silent.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/avrg_silent.cc.o -MF CMakeFiles/avrg_silent.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/avrg_silent.cc.o.d -o CMakeFiles/avrg_silent.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/avrg_silent.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/avrg_silent.cc [188/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/supercharge ../../bin/supercharge && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/supercharge ../../bin/supercharge.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/supercharge ../../bin/supercharge.default.macosclangrelease [189/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/zinc2_homodimer_design.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc2_homodimer_design.cc.o -o zinc2_homodimer_design -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [190/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/validate_silent.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/validate_silent.cc.o -MF CMakeFiles/validate_silent.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/validate_silent.cc.o.d -o CMakeFiles/validate_silent.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/validate_silent.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/validate_silent.cc [191/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/avrg_silent.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/avrg_silent.cc.o -o avrg_silent -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) [192/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/zinc2_homodimer_design ../../bin/zinc2_homodimer_design && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/zinc2_homodimer_design ../../bin/zinc2_homodimer_design.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/zinc2_homodimer_design ../../bin/zinc2_homodimer_design.default.macosclangrelease [193/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/avrg_silent ../../bin/avrg_silent && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/avrg_silent ../../bin/avrg_silent.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/avrg_silent ../../bin/avrg_silent.default.macosclangrelease [194/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/ensemble_generator_score12_sidechain_ver2.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ddg/ensemble_generator_score12_sidechain_ver2.cc.o -MF 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-I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/cartesian_ddg.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ddg/cartesian_ddg.cc.o -MF CMakeFiles/cartesian_ddg.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ddg/cartesian_ddg.cc.o.d -o CMakeFiles/cartesian_ddg.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ddg/cartesian_ddg.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ddg/cartesian_ddg.cc [196/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/validate_silent.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/validate_silent.cc.o -o validate_silent -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [197/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/validate_silent ../../bin/validate_silent && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/validate_silent ../../bin/validate_silent.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/validate_silent ../../bin/validate_silent.default.macosclangrelease [198/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names 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-fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/ensemble_generator_score12_sidechain_ver2.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ddg/ensemble_generator_score12_sidechain_ver2.cc.o -o ensemble_generator_score12_sidechain_ver2 -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [200/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cartesian_ddg.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ddg/cartesian_ddg.cc.o -o cartesian_ddg -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [201/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/grower_prep ../../bin/grower_prep && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/grower_prep ../../bin/grower_prep.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/grower_prep ../../bin/grower_prep.default.macosclangrelease [202/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/dgdp ../../bin/dgdp && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/dgdp ../../bin/dgdp.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/dgdp ../../bin/dgdp.default.macosclangrelease [203/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/ensemble_generator_score12_sidechain_ver2 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/Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cartesian_ddg ../../bin/cartesian_ddg && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cartesian_ddg ../../bin/cartesian_ddg.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cartesian_ddg ../../bin/cartesian_ddg.default.macosclangrelease [205/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS 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/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/zinc_heterodimer_design.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc_heterodimer_design.cc.o -MF CMakeFiles/zinc_heterodimer_design.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc_heterodimer_design.cc.o.d -o CMakeFiles/zinc_heterodimer_design.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc_heterodimer_design.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc_heterodimer_design.cc [207/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/enzyme_design ../../bin/enzyme_design && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/enzyme_design ../../bin/enzyme_design.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/enzyme_design ../../bin/enzyme_design.default.macosclangrelease [208/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/CstfileToTheozymePDB ../../bin/CstfileToTheozymePDB && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/CstfileToTheozymePDB ../../bin/CstfileToTheozymePDB.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/CstfileToTheozymePDB ../../bin/CstfileToTheozymePDB.default.macosclangrelease [209/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/identify_ligand_motifs ../../bin/identify_ligand_motifs && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/identify_ligand_motifs ../../bin/identify_ligand_motifs.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/identify_ligand_motifs ../../bin/identify_ligand_motifs.default.macosclangrelease [210/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/mr_protocols.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/electron_density/mr_protocols.cc.o -o mr_protocols -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [211/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/AnchoredDesign.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/interface_design/anchored_design/AnchoredDesign.cc.o -o AnchoredDesign -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [212/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/remove_duplicate_motifs ../../bin/remove_duplicate_motifs && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/remove_duplicate_motifs ../../bin/remove_duplicate_motifs.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/remove_duplicate_motifs ../../bin/remove_duplicate_motifs.default.macosclangrelease [213/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mr_protocols ../../bin/mr_protocols && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mr_protocols ../../bin/mr_protocols.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mr_protocols ../../bin/mr_protocols.default.macosclangrelease [214/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/zinc_heterodimer_design.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/zinc_heterodimer_design.cc.o -o zinc_heterodimer_design -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [215/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/make_ray_files.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/darc/make_ray_files.cc.o -MF CMakeFiles/make_ray_files.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/darc/make_ray_files.cc.o.d -o CMakeFiles/make_ray_files.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/darc/make_ray_files.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/darc/make_ray_files.cc [216/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/MakeSegmentFile.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/pose_sewing/MakeSegmentFile.cc.o -o MakeSegmentFile -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [217/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/AnchoredDesign ../../bin/AnchoredDesign && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/AnchoredDesign ../../bin/AnchoredDesign.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/AnchoredDesign ../../bin/AnchoredDesign.default.macosclangrelease [218/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/DNA_methylation ../../bin/DNA_methylation && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/DNA_methylation ../../bin/DNA_methylation.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/DNA_methylation ../../bin/DNA_methylation.default.macosclangrelease [219/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/N-terminal_acetylation ../../bin/N-terminal_acetylation && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/N-terminal_acetylation ../../bin/N-terminal_acetylation.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/N-terminal_acetylation ../../bin/N-terminal_acetylation.default.macosclangrelease [220/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/score_aln.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/score_aln.cc.o -MF CMakeFiles/score_aln.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/score_aln.cc.o.d -o CMakeFiles/score_aln.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/score_aln.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/score_aln.cc [221/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/zinc_heterodimer_design ../../bin/zinc_heterodimer_design && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/zinc_heterodimer_design ../../bin/zinc_heterodimer_design.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/zinc_heterodimer_design ../../bin/zinc_heterodimer_design.default.macosclangrelease [222/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/MakeSegmentFile ../../bin/MakeSegmentFile && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/MakeSegmentFile ../../bin/MakeSegmentFile.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/MakeSegmentFile ../../bin/MakeSegmentFile.default.macosclangrelease [223/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/phosphorylation ../../bin/phosphorylation && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/phosphorylation ../../bin/phosphorylation.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/phosphorylation ../../bin/phosphorylation.default.macosclangrelease [224/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/glycosyltransfer ../../bin/glycosyltransfer && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/glycosyltransfer ../../bin/glycosyltransfer.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/glycosyltransfer ../../bin/glycosyltransfer.default.macosclangrelease [225/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/make_ray_files.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/darc/make_ray_files.cc.o -o make_ray_files -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [226/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_denovo.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/rna_denovo.cc.o -o rna_denovo -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [227/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/score_aln.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/score_aln.cc.o -o score_aln -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [228/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/erraser_minimizer ../../bin/erraser_minimizer && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/erraser_minimizer ../../bin/erraser_minimizer.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/erraser_minimizer ../../bin/erraser_minimizer.default.macosclangrelease [229/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_design.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/rna_design.cc.o -o rna_design -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [230/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/erraser2.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/erraser/erraser2.cc.o -o erraser2 -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [231/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/make_ray_files ../../bin/make_ray_files && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/make_ray_files ../../bin/make_ray_files.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/make_ray_files ../../bin/make_ray_files.default.macosclangrelease [232/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_thread.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/thread/rna_thread.cc.o -o rna_thread -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [233/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_denovo ../../bin/rna_denovo && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_denovo ../../bin/rna_denovo.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_denovo ../../bin/rna_denovo.default.macosclangrelease [234/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/score_aln ../../bin/score_aln && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/score_aln ../../bin/score_aln.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/score_aln ../../bin/score_aln.default.macosclangrelease [235/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_design ../../bin/rna_design && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_design ../../bin/rna_design.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_design ../../bin/rna_design.default.macosclangrelease [236/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/erraser2 ../../bin/erraser2 && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/erraser2 ../../bin/erraser2.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/erraser2 ../../bin/erraser2.default.macosclangrelease [237/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/analyze_base_pairing ../../bin/analyze_base_pairing && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/analyze_base_pairing ../../bin/analyze_base_pairing.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/analyze_base_pairing ../../bin/analyze_base_pairing.default.macosclangrelease [238/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_thread_and_minimize.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/thread/rna_thread_and_minimize.cc.o -o rna_thread_and_minimize -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [239/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_thread ../../bin/rna_thread && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_thread ../../bin/rna_thread.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_thread ../../bin/rna_thread.default.macosclangrelease [240/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cs_rosetta_rna.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/cs_rosetta_rna.cc.o -o cs_rosetta_rna -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [241/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/nucleobase_sample_around.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/nucleobase_sample_around.cc.o -o nucleobase_sample_around -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [242/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_cluster.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/rna_cluster.cc.o -o rna_cluster -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) [243/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_thread_and_minimize ../../bin/rna_thread_and_minimize && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_thread_and_minimize ../../bin/rna_thread_and_minimize.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_thread_and_minimize ../../bin/rna_thread_and_minimize.default.macosclangrelease [244/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/rna_database.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/rna/util/rna_database.cc.o -o rna_database -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [245/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cs_rosetta_rna ../../bin/cs_rosetta_rna && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cs_rosetta_rna ../../bin/cs_rosetta_rna.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/cs_rosetta_rna ../../bin/cs_rosetta_rna.default.macosclangrelease [246/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/full_length_model.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/full_length_model.cc.o -MF CMakeFiles/full_length_model.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/full_length_model.cc.o.d -o CMakeFiles/full_length_model.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/full_length_model.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/full_length_model.cc [247/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_cluster ../../bin/rna_cluster && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_cluster ../../bin/rna_cluster.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_cluster ../../bin/rna_cluster.default.macosclangrelease [248/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/nucleobase_sample_around ../../bin/nucleobase_sample_around && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/nucleobase_sample_around ../../bin/nucleobase_sample_around.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/nucleobase_sample_around ../../bin/nucleobase_sample_around.default.macosclangrelease [249/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_database ../../bin/rna_database && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_database ../../bin/rna_database.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/rna_database ../../bin/rna_database.default.macosclangrelease [250/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/template_features.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/template_features.cc.o -MF CMakeFiles/template_features.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/template_features.cc.o.d -o CMakeFiles/template_features.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/template_features.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/template_features.cc [251/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/full_length_model.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/full_length_model.cc.o -o full_length_model -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [252/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/full_length_model ../../bin/full_length_model && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/full_length_model ../../bin/full_length_model.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/full_length_model ../../bin/full_length_model.default.macosclangrelease [253/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/template_features.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/template_features.cc.o -o template_features -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than 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/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/coupled_moves.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/coupled_moves/coupled_moves.cc.o -MF 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-I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe 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/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names 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-DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/score_aln2.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/comparative_modeling/score_aln2.cc.o -o score_aln2 -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [261/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/coupled_moves ../../bin/coupled_moves && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/coupled_moves ../../bin/coupled_moves.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/coupled_moves ../../bin/coupled_moves.default.macosclangrelease [262/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/fit_helix_in_map ../../bin/fit_helix_in_map && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/fit_helix_in_map ../../bin/fit_helix_in_map.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/fit_helix_in_map ../../bin/fit_helix_in_map.default.macosclangrelease [263/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/beta_peptide_modeling.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/beta_peptide_modeling.cc.o -MF CMakeFiles/beta_peptide_modeling.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/beta_peptide_modeling.cc.o.d -o CMakeFiles/beta_peptide_modeling.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/beta_peptide_modeling.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/beta_peptide_modeling.cc [264/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/score_aln2 ../../bin/score_aln2 && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/score_aln2 ../../bin/score_aln2.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/score_aln2 ../../bin/score_aln2.default.macosclangrelease [265/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/beta_peptide_modeling.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/beta_peptide_modeling.cc.o -o beta_peptide_modeling -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [266/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/beta_peptide_modeling ../../bin/beta_peptide_modeling && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/beta_peptide_modeling ../../bin/beta_peptide_modeling.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/beta_peptide_modeling ../../bin/beta_peptide_modeling.default.macosclangrelease [267/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src 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-pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I 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libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [276/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/spheregrinder ../../bin/spheregrinder && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/spheregrinder ../../bin/spheregrinder.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/spheregrinder ../../bin/spheregrinder.default.macosclangrelease [277/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/sequence_recovery.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/sequence_recovery.cc.o -o sequence_recovery -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [278/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/iterhybrid_selector ../../bin/iterhybrid_selector && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/iterhybrid_selector ../../bin/iterhybrid_selector.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/iterhybrid_selector ../../bin/iterhybrid_selector.default.macosclangrelease [279/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/sequence_recovery ../../bin/sequence_recovery && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/sequence_recovery ../../bin/sequence_recovery.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/sequence_recovery ../../bin/sequence_recovery.default.macosclangrelease [280/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/validate_database.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/internal/validate_database.cc.o -MF CMakeFiles/validate_database.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/internal/validate_database.cc.o.d -o CMakeFiles/validate_database.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/internal/validate_database.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/internal/validate_database.cc [281/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/generate_database_cache.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/internal/generate_database_cache.cc.o -o generate_database_cache -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [282/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/generate_database_cache ../../bin/generate_database_cache && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/generate_database_cache ../../bin/generate_database_cache.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/generate_database_cache ../../bin/generate_database_cache.default.macosclangrelease [283/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/validate_database.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/internal/validate_database.cc.o -o validate_database -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [284/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/drrafter_error_estimation.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/DRRAFTER/drrafter_error_estimation.cc.o -MF CMakeFiles/drrafter_error_estimation.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/DRRAFTER/drrafter_error_estimation.cc.o.d -o CMakeFiles/drrafter_error_estimation.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/DRRAFTER/drrafter_error_estimation.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/DRRAFTER/drrafter_error_estimation.cc [285/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/validate_database ../../bin/validate_database && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/validate_database ../../bin/validate_database.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/validate_database ../../bin/validate_database.default.macosclangrelease [286/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/drrafter_error_estimation.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/DRRAFTER/drrafter_error_estimation.cc.o -o drrafter_error_estimation -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [287/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/drrafter_error_estimation ../../bin/drrafter_error_estimation && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/drrafter_error_estimation ../../bin/drrafter_error_estimation.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/drrafter_error_estimation ../../bin/drrafter_error_estimation.default.macosclangrelease [288/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe 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-fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/ligand_dock.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ligand_docking/ligand_dock.cc.o -o ligand_dock -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [290/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/ligand_dock ../../bin/ligand_dock && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/ligand_dock ../../bin/ligand_dock.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/ligand_dock ../../bin/ligand_dock.default.macosclangrelease [291/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I 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-DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/count_cycpep_sequences.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/cyclic_peptide/count_cycpep_sequences.cc.o -MF CMakeFiles/count_cycpep_sequences.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/cyclic_peptide/count_cycpep_sequences.cc.o.d -o CMakeFiles/count_cycpep_sequences.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/cyclic_peptide/count_cycpep_sequences.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/cyclic_peptide/count_cycpep_sequences.cc [293/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/mpi_msd.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/design/mpi_msd.cc.o -o mpi_msd -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [294/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mpi_msd ../../bin/mpi_msd && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mpi_msd ../../bin/mpi_msd.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/mpi_msd ../../bin/mpi_msd.default.macosclangrelease [295/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/count_cycpep_sequences.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/cyclic_peptide/count_cycpep_sequences.cc.o -o count_cycpep_sequences -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [296/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/count_cycpep_sequences ../../bin/count_cycpep_sequences && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/count_cycpep_sequences ../../bin/count_cycpep_sequences.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/count_cycpep_sequences ../../bin/count_cycpep_sequences.default.macosclangrelease [297/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/MakeRotLib.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ncaa_utilities/MakeRotLib.cc.o -MF CMakeFiles/MakeRotLib.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ncaa_utilities/MakeRotLib.cc.o.d -o CMakeFiles/MakeRotLib.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ncaa_utilities/MakeRotLib.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ncaa_utilities/MakeRotLib.cc [298/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/MakeRotLib.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ncaa_utilities/MakeRotLib.cc.o -o MakeRotLib -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [299/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/calc_nmr_tensor.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/nmr/calc_nmr_tensor.cc.o -MF CMakeFiles/calc_nmr_tensor.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/nmr/calc_nmr_tensor.cc.o.d -o CMakeFiles/calc_nmr_tensor.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/nmr/calc_nmr_tensor.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/nmr/calc_nmr_tensor.cc [300/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/extract_atomtree_diffs.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ligand_docking/extract_atomtree_diffs.cc.o -MF CMakeFiles/extract_atomtree_diffs.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ligand_docking/extract_atomtree_diffs.cc.o.d -o CMakeFiles/extract_atomtree_diffs.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ligand_docking/extract_atomtree_diffs.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ligand_docking/extract_atomtree_diffs.cc [301/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/MakeRotLib ../../bin/MakeRotLib && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/MakeRotLib ../../bin/MakeRotLib.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/MakeRotLib ../../bin/MakeRotLib.default.macosclangrelease [302/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/calc_nmr_tensor.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/nmr/calc_nmr_tensor.cc.o -o calc_nmr_tensor -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [303/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/extract_atomtree_diffs.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ligand_docking/extract_atomtree_diffs.cc.o -o extract_atomtree_diffs -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [304/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/calc_nmr_tensor ../../bin/calc_nmr_tensor && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/calc_nmr_tensor ../../bin/calc_nmr_tensor.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/calc_nmr_tensor ../../bin/calc_nmr_tensor.default.macosclangrelease [305/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/extract_atomtree_diffs ../../bin/extract_atomtree_diffs && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/extract_atomtree_diffs ../../bin/extract_atomtree_diffs.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/extract_atomtree_diffs ../../bin/extract_atomtree_diffs.default.macosclangrelease [306/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY 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/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/recon_design/recon.cc [313/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/DARC.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/darc/DARC.cc.o -o DARC -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [314/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/ligand_rpkmin ../../bin/ligand_rpkmin && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/ligand_rpkmin ../../bin/ligand_rpkmin.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/ligand_rpkmin ../../bin/ligand_rpkmin.default.macosclangrelease [315/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/DARC ../../bin/DARC && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/DARC ../../bin/DARC.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/DARC ../../bin/DARC.default.macosclangrelease [316/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/recon.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/recon_design/recon.cc.o -o recon -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [317/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/recon ../../bin/recon && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/recon ../../bin/recon.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/recon ../../bin/recon.default.macosclangrelease [318/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/AnchoredPDBCreator.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/interface_design/anchored_design/AnchoredPDBCreator.cc.o -MF CMakeFiles/AnchoredPDBCreator.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/interface_design/anchored_design/AnchoredPDBCreator.cc.o.d -o 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was built for newer macOS version (12.0) than being linked (10.10) [320/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem 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-DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/thermal_sampler.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/recces/legacy/thermal_sampler.cc.o -o thermal_sampler -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod 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libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [328/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/recces_turner.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/recces/legacy/recces_turner.cc.o -o recces_turner -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [329/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/select_best_unique_ligand_poses.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ligand_docking/select_best_unique_ligand_poses.cc.o -o select_best_unique_ligand_poses -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [330/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/thermal_sampler ../../bin/thermal_sampler && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/thermal_sampler ../../bin/thermal_sampler.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/thermal_sampler ../../bin/thermal_sampler.default.macosclangrelease [331/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/recces_turner ../../bin/recces_turner && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/recces_turner ../../bin/recces_turner.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/recces_turner ../../bin/recces_turner.default.macosclangrelease [332/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/select_best_unique_ligand_poses ../../bin/select_best_unique_ligand_poses && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/select_best_unique_ligand_poses ../../bin/select_best_unique_ligand_poses.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/select_best_unique_ligand_poses ../../bin/select_best_unique_ligand_poses.default.macosclangrelease [333/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/pocket_measure.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/pocket/pocket_measure.cc.o -MF CMakeFiles/pocket_measure.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/pocket/pocket_measure.cc.o.d -o CMakeFiles/pocket_measure.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/pocket/pocket_measure.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/pocket/pocket_measure.cc [334/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/UnfoldedStateEnergyCalculator.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ncaa_utilities/UnfoldedStateEnergyCalculator.cc.o -MF CMakeFiles/UnfoldedStateEnergyCalculator.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ncaa_utilities/UnfoldedStateEnergyCalculator.cc.o.d -o CMakeFiles/UnfoldedStateEnergyCalculator.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ncaa_utilities/UnfoldedStateEnergyCalculator.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ncaa_utilities/UnfoldedStateEnergyCalculator.cc [335/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/pocket_measure.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/pocket/pocket_measure.cc.o -o pocket_measure -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) [336/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/pocket_measure ../../bin/pocket_measure && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/pocket_measure ../../bin/pocket_measure.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/pocket_measure ../../bin/pocket_measure.default.macosclangrelease [337/671] : && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/UnfoldedStateEnergyCalculator.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/ncaa_utilities/UnfoldedStateEnergyCalculator.cc.o -o UnfoldedStateEnergyCalculator -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -L/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -L/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/lib -Wl,-rpath,/usr/X11/lib -Wl,-rpath,/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics libdevel.dylib libprotocols.8.dylib libprotocols.7.dylib libprotocols_e.6.dylib libprotocols_d.6.dylib libprotocols_c.6.dylib libprotocols_b.6.dylib libprotocols_a.6.dylib libprotocols_h.5.dylib libprotocols_g.5.dylib libprotocols_f.5.dylib libprotocols_e.5.dylib libprotocols_d.5.dylib libprotocols_c.5.dylib libprotocols_b.5.dylib libprotocols_a.5.dylib libprotocols.4.dylib libprotocols.3.dylib libprotocols_b.2.dylib libprotocols_a.2.dylib libprotocols.1.dylib libcore.6.dylib libcore.5.dylib libcore.4.dylib libcore.3.dylib libcore.2.dylib libcore.1.dylib libbasic.dylib libnumeric.dylib libutility.dylib libObjexxFCL.dylib -lz -ldl -lstdc++ libcifparse.dylib liblibxml2.dylib librdkit.dylib libcmaes.dylib libcppdb.dylib libsqlite3.dylib && : ld: warning: directory not found for option '-L/usr/X11/lib' ld: warning: dylib (liblibxml2.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libcmaes.dylib) was built for newer macOS version (12.0) than being linked (10.10) ld: warning: dylib (libsqlite3.dylib) was built for newer macOS version (12.0) than being linked (10.10) [338/671] cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E make_directory ../../bin/ && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/UnfoldedStateEnergyCalculator ../../bin/UnfoldedStateEnergyCalculator && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/UnfoldedStateEnergyCalculator ../../bin/UnfoldedStateEnergyCalculator.macosclangrelease && /Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/site-packages/cmake/data/CMake.app/Contents/bin/cmake -E create_symlink /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/UnfoldedStateEnergyCalculator ../../bin/UnfoldedStateEnergyCalculator.default.macosclangrelease [339/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/r_noe_assign.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/nmr/r_noe_assign.cc.o -MF CMakeFiles/r_noe_assign.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/nmr/r_noe_assign.cc.o.d -o CMakeFiles/r_noe_assign.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/nmr/r_noe_assign.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/nmr/r_noe_assign.cc [340/671] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/ligand_discovery_search_protocol.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc.o -MF CMakeFiles/ligand_discovery_search_protocol.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc.o.d -o CMakeFiles/ligand_discovery_search_protocol.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc FAILED: CMakeFiles/ligand_discovery_search_protocol.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DGL_GRAPHICS -DMAC -DNDEBUG -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../.. -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src -I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/ligand_discovery_search_protocol.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc.o -MF CMakeFiles/ligand_discovery_search_protocol.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc.o.d -o CMakeFiles/ligand_discovery_search_protocol.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc:250:9: error: use of undeclared identifier 'i' for (i = 0; i < option[ OptionKeys::motifs::protein_discovery_locus ].size(); ++i) ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc:250:16: error: use of undeclared identifier 'i' for (i = 0; i < option[ OptionKeys::motifs::protein_discovery_locus ].size(); ++i) ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc:250:84: error: use of undeclared identifier 'i' for (i = 0; i < option[ OptionKeys::motifs::protein_discovery_locus ].size(); ++i) ^ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc:252:88: error: use of undeclared identifier 'i' discovery_position.push_back(option[ OptionKeys::motifs::protein_discovery_locus ][i]); ^ 4 errors generated. 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-I/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../src/platform/macos -I/usr/X11/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/include -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/rdkit -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/boost_submod -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/cxxtest -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/dbio/sqlite3 -isystem /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics/../../external/libxml2/include -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -std=c++11 -stdlib=libc++ -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -I src/platform/macos/64/clang/6.1 -I src/platform/macos/64/clang -I src/platform/macos/64 -O3 -pipe -ffast-math -fno-finite-math-only -funroll-loops -ftemplate-depth=250 -mmacosx-version-min=10.10 -Werror=reorder -Werror=address -Werror=char-subscripts -Werror=comment -Werror=nonnull -Werror=type-limits -Werror=parentheses -Werror=ignored-qualifiers -Werror=enum-compare -MD -MT CMakeFiles/pepspec.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/pepspec/pepspec.cc.o -MF CMakeFiles/pepspec.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/pepspec/pepspec.cc.o.d -o CMakeFiles/pepspec.dir/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/pepspec/pepspec.cc.o -c /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/apps/public/pepspec/pepspec.cc ninja: build stopped: subcommand failed. Traceback (most recent call last): File "/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/./ninja_build.py", line 132, in <module> subprocess.check_call(ninja_command) File "/Users/benchmark/prefix/b3.python-3.10.5/lib/python3.10/subprocess.py", line 369, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['ninja', '-C', '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/cmake/build_graphics', '-j', '32', '-v']' returned non-zero exit status 1.

Sub-Tests Results

All sub-tests

JSON output

{}