linking with clang++ on OS X generates lots of symbol not found errors

Question

I'm trying to compile some C++ code (including C++11 features) on OS X 10.8 using the clang++ compiler. I have a makefile that generates the object files OK, then on the command:

clang++  -o Analysis.so -shared DataFile.o CR39DataFile.o

I get tons of errors about symbol(s) not found for architecture x86_64. The code works fine on a *nix system using g++ and changing the compiler flags appropriately for C++11 support. To compile the *.o I am doing it like:

clang++ -c -Wall -std=c++11 -stdlib=libc++ -I../src ../src/DataFile.cc

Edit: output of the linking command is:

clang++  -o Analysis.so -shared DataFile.o CR39DataFile.o
Undefined symbols for architecture x86_64:
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::find(char const*, unsigned long, unsigned long) const", referenced from:
CR39DataFile::read_thread(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in CR39DataFile.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::find(char, unsigned long) const", referenced from:
CR39DataFile::trim(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in CR39DataFile.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::compare(char const*) const", referenced from:
CR39DataFile::read_thread(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in CR39DataFile.o
"std::__1::__vector_base_common<true>::__throw_length_error() const", referenced from:
std::__1::vector<frame*, std::__1::allocator<frame*> >::__append(unsigned long) in CR39DataFile.o
std::__1::vector<std::__1::vector<frame*, std::__1::allocator<frame*> >*, std::__1::allocator<std::__1::vector<frame*, std::__1::allocator<frame*> >*> >::__append(unsigned long) in CR39DataFile.o
"std::__1::__vector_base_common<true>::__throw_out_of_range() const", referenced from:
std::__1::vector<std::__1::vector<frame*, std::__1::allocator<frame*> >*, std::__1::allocator<std::__1::vector<frame*, std::__1::allocator<frame*> >*> >::at(unsigned long) in CR39DataFile.o
std::__1::vector<frame*, std::__1::allocator<frame*> >::at(unsigned long) in CR39DataFile.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::erase(unsigned long, unsigned long)", referenced from:
CR39DataFile::trim(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in CR39DataFile.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::assign(char const*)", referenced from:
CR39DataFile::CR39DataFile() in CR39DataFile.o
CR39DataFile::clear() in CR39DataFile.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::insert(unsigned long, unsigned long, char)", referenced from:
CR39DataFile::read_thread(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in CR39DataFile.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::resize(unsigned long, char)", referenced from:
CR39DataFile::read_thread(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in CR39DataFile.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::reserve(unsigned long)", referenced from:
CR39DataFile::read_thread(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in CR39DataFile.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::basic_string(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
DataFile::read(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, bool) in DataFile.o
DataFile::write(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, bool) in DataFile.o
std::__1::thread::thread<bool (DataFile::*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >), DataFile*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, void>(bool (DataFile::*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >)&&, DataFile*&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&&&) in DataFile.o
CR39DataFile::read_thread(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in CR39DataFile.o
CR39DataFile::write_thread(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in CR39DataFile.o
CR39DataFile::write_thread(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, float, float, float, float, float, float, float, float, float, float) in CR39DataFile.o
CR39DataFile::write_thread(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, float, float, float, float, float, float) in CR39DataFile.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::basic_string(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long, unsigned long, std::__1::allocator<char> const&)", referenced from:
CR39DataFile::read_thread(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in CR39DataFile.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_string()", referenced from:
DataFile::~DataFile() in DataFile.o
DataFile::read(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, bool) in DataFile.o
DataFile::write(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, bool) in DataFile.o
std::__1::thread::thread<bool (DataFile::*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >), DataFile*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, void>(bool (DataFile::*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >)&&, DataFile*&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&&&) in DataFile.o
void* std::__1::__thread_proxy<std::__1::tuple<bool (DataFile::*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >), DataFile*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > >(void*) in DataFile.o
std::__1::__tuple_leaf<2ul, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, false>::~__tuple_leaf() in DataFile.o
CR39DataFile::CR39DataFile() in CR39DataFile.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::operator=(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
CR39DataFile::set_file_path(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in CR39DataFile.o
CR39DataFile::set_file_auxpath(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in CR39DataFile.o
"std::__1::__thread_struct::__thread_struct()", referenced from:
void* std::__1::__thread_proxy<std::__1::tuple<bool (DataFile::*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >), DataFile*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > >(void*) in DataFile.o
"std::__1::__thread_struct::~__thread_struct()", referenced from:
std::__1::__thread_specific_ptr<std::__1::__thread_struct>::reset(std::__1::__thread_struct*) in DataFile.o
"std::__1::__thread_local_data()", referenced from:
void* std::__1::__thread_proxy<std::__1::tuple<bool (DataFile::*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >), DataFile*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > >(void*) in DataFile.o
"std::__1::__throw_system_error(int, char const*)", referenced from:
std::__1::thread::thread<bool (DataFile::*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >), DataFile*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, void>(bool (DataFile::*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >)&&, DataFile*&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&&&) in DataFile.o
"std::__1::thread::~thread()", referenced from:
DataFile::cleanup_file_io() in DataFile.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [Analysis.so] Error 1

Answer 1

I suspect this issue is because of the two C++ runtime libraries available under OS X. Use the following to link the dynamic library:

clang++ -stdlib=libc++ -o Analysis.dylib -shared DataFile.o CR39DataFile.o

(the -stdlib=libc++ being the key difference). I think the default C++ runtime is the GNU implementation which is confusing the linker as you compiled with the libc++ implementation.