Generating bindings...
cd /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/ && /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/prefix/llvm-3.8/llvm/build_release_38.linux.head.release/bin/binder --config ./rosetta.config --root-module rosetta --prefix /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/ /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/all_rosetta_includes.hh -- -std=c++11  -isystem external -isystem external/include -isystem external/boost_1_55_0 -isystem external/dbio -isystem external/dbio/sqlite3 -isystem external/libxml2/include -Isrc -Isrc/platform/linux  -DPYROSETTA -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG
In file included from /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/all_rosetta_includes.hh:100:
In file included from src/basic/ComparingTracer.hh:19:
In file included from src/basic/Tracer.hh:23:
In file included from src/utility/vector1.hh:23:
src/utility/vectorL.hh:132:15: error: no member named 'shrink_to_fit' in 'std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::shrink_to_fit;
              ~~~~~~~^
src/utility/vector1.hh:43:9: note: in instantiation of template class 'utility::vectorL<1, std::basic_string<char>, std::allocator<std::basic_string<char> > >' requested here
        public vectorL< 1, T, A >
               ^
src/basic/Tracer.hh:120:32: note: in instantiation of template class 'utility::vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >' requested here
        utility::vector1<std::string> muted;
                                      ^
In file included from /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/all_rosetta_includes.hh:100:
In file included from src/basic/ComparingTracer.hh:19:
In file included from src/basic/Tracer.hh:23:
src/utility/vector1.hh:91:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::assign;
              ^~~~~~~
src/basic/Tracer.hh:120:32: note: in instantiation of template class 'utility::vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >' requested here
        utility::vector1<std::string> muted;
                                      ^
In file included from /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/all_rosetta_includes.hh:100:
In file included from src/basic/ComparingTracer.hh:19:
In file included from src/basic/Tracer.hh:23:
src/utility/vector1.hh:92:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::at;
              ^~~~~~~
src/utility/vector1.hh:93:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::back;
              ^~~~~~~
src/utility/vector1.hh:94:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::begin;
              ^~~~~~~
src/utility/vector1.hh:95:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::capacity;
              ^~~~~~~
src/utility/vector1.hh:96:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::cbegin;
              ^~~~~~~
src/utility/vector1.hh:97:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::cend;
              ^~~~~~~
src/utility/vector1.hh:98:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::crbegin;
              ^~~~~~~
src/utility/vector1.hh:99:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::crend;
              ^~~~~~~
src/utility/vector1.hh:100:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::clear;
              ^~~~~~~
src/utility/vector1.hh:101:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::emplace;
              ^~~~~~~
src/utility/vector1.hh:102:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::emplace_back;
              ^~~~~~~
src/utility/vector1.hh:103:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::empty;
              ^~~~~~~
src/utility/vector1.hh:104:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::end;
              ^~~~~~~
src/utility/vector1.hh:105:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::erase;
              ^~~~~~~
src/utility/vector1.hh:106:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::front;
              ^~~~~~~
src/utility/vector1.hh:107:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::get_allocator;
              ^~~~~~~
src/utility/vector1.hh:108:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::insert;
              ^~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
/bin/sh: line 1: 29050 Segmentation fault      /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/prefix/llvm-3.8/llvm/build_release_38.linux.head.release/bin/binder --config ./rosetta.config --root-module rosetta --prefix /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/ /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/all_rosetta_includes.hh -- -std=c++11 -isystem external -isystem external/include -isystem external/boost_1_55_0 -isystem external/dbio -isystem external/dbio/sqlite3 -isystem external/libxml2/include -Isrc -Isrc/platform/linux -DPYROSETTA -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG


Encounter error while executing: cd /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/ && /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/prefix/llvm-3.8/llvm/build_release_38.linux.head.release/bin/binder --config ./rosetta.config --root-module rosetta --prefix /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/ /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/all_rosetta_includes.hh -- -std=c++11  -isystem external -isystem external/include -isystem external/boost_1_55_0 -isystem external/dbio -isystem external/dbio/sqlite3 -isystem external/libxml2/include -Isrc -Isrc/platform/linux  -DPYROSETTA -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG

Encounter error while executing: cd /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/ && /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/prefix/llvm-3.8/llvm/build_release_38.linux.head.release/bin/binder --config ./rosetta.config --root-module rosetta --prefix /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/ /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/all_rosetta_includes.hh -- -std=c++11  -isystem external -isystem external/include -isystem external/boost_1_55_0 -isystem external/dbio -isystem external/dbio/sqlite3 -isystem external/libxml2/include -Isrc -Isrc/platform/linux  -DPYROSETTA -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG
In file included from /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/all_rosetta_includes.hh:100:
In file included from src/basic/ComparingTracer.hh:19:
In file included from src/basic/Tracer.hh:23:
In file included from src/utility/vector1.hh:23:
src/utility/vectorL.hh:132:15: error: no member named 'shrink_to_fit' in 'std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::shrink_to_fit;
              ~~~~~~~^
src/utility/vector1.hh:43:9: note: in instantiation of template class 'utility::vectorL<1, std::basic_string<char>, std::allocator<std::basic_string<char> > >' requested here
        public vectorL< 1, T, A >
               ^
src/basic/Tracer.hh:120:32: note: in instantiation of template class 'utility::vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >' requested here
        utility::vector1<std::string> muted;
                                      ^
In file included from /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/all_rosetta_includes.hh:100:
In file included from src/basic/ComparingTracer.hh:19:
In file included from src/basic/Tracer.hh:23:
src/utility/vector1.hh:91:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::assign;
              ^~~~~~~
src/basic/Tracer.hh:120:32: note: in instantiation of template class 'utility::vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >' requested here
        utility::vector1<std::string> muted;
                                      ^
In file included from /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/all_rosetta_includes.hh:100:
In file included from src/basic/ComparingTracer.hh:19:
In file included from src/basic/Tracer.hh:23:
src/utility/vector1.hh:92:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::at;
              ^~~~~~~
src/utility/vector1.hh:93:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::back;
              ^~~~~~~
src/utility/vector1.hh:94:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::begin;
              ^~~~~~~
src/utility/vector1.hh:95:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::capacity;
              ^~~~~~~
src/utility/vector1.hh:96:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::cbegin;
              ^~~~~~~
src/utility/vector1.hh:97:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::cend;
              ^~~~~~~
src/utility/vector1.hh:98:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::crbegin;
              ^~~~~~~
src/utility/vector1.hh:99:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::crend;
              ^~~~~~~
src/utility/vector1.hh:100:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::clear;
              ^~~~~~~
src/utility/vector1.hh:101:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::emplace;
              ^~~~~~~
src/utility/vector1.hh:102:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::emplace_back;
              ^~~~~~~
src/utility/vector1.hh:103:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::empty;
              ^~~~~~~
src/utility/vector1.hh:104:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::end;
              ^~~~~~~
src/utility/vector1.hh:105:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::erase;
              ^~~~~~~
src/utility/vector1.hh:106:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::front;
              ^~~~~~~
src/utility/vector1.hh:107:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::get_allocator;
              ^~~~~~~
src/utility/vector1.hh:108:8: error: using declaration refers into 'super::', which is not a base class of 'vector1<std::basic_string<char>, std::allocator<std::basic_string<char> > >'
        using super::insert;
              ^~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
/bin/sh: line 1: 29050 Segmentation fault      /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/prefix/llvm-3.8/llvm/build_release_38.linux.head.release/bin/binder --config ./rosetta.config --root-module rosetta --prefix /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/ /work/hpcf/jcbonilla/PyRosetta/rosetta_src_2017.08.59291_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release/source/all_rosetta_includes.hh -- -std=c++11 -isystem external -isystem external/include -isystem external/boost_1_55_0 -isystem external/dbio -isystem external/dbio/sqlite3 -isystem external/libxml2/include -Isrc -Isrc/platform/linux -DPYROSETTA -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG