Hi Christoph,
This problem still persist with clang ver 6.0, but now linking against lib
boost_program_options.dylib is broken:
[ 96%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/linalg/gsl/svd.cc.o
cd /Volumes/Home/Work/VOTCA/tools/src/libtools && /usr/bin/c++
-Dvotca_tools_EXPORTS -O3 -DNDEBUG -fPIC
-I/Volumes/Home/Work/VOTCA/tools/include -I/usr/local/boost/include
-I/usr/local/fftw/include -I/usr/local/gsl/include
-I/Volumes/Home/Work/VOTCA/tools/src/libtools
-I/Volumes/Home/Work/VOTCA/tools/include/votca/tools -o
CMakeFiles/votca_tools.dir/linalg/gsl/svd.cc.o -c
/Volumes/Home/Work/VOTCA/tools/src/libtools/linalg/gsl/svd.cc
*Linking CXX shared library libvotca_tools.dylib*
cd /Volumes/Home/Work/VOTCA/tools/src/libtools &&
/Applications/CMake.app/Contents/bin/cmake -E cmake_link_script
CMakeFiles/votca_tools.dir/link.txt --verbose=1
/usr/bin/c++ -O3 -DNDEBUG -dynamiclib -Wl,-headerpad_max_install_names
-compatibility_version 3.0.0 -o libvotca_tools.3.dylib -install_name
/Volumes/Home/Work/VOTCA/tools/src/libtools/libvotca_tools.3.dylib
CMakeFiles/votca_tools.dir/akimaspline.cc.o
CMakeFiles/votca_tools.dir/application.cc.o
CMakeFiles/votca_tools.dir/colors.cc.o
CMakeFiles/votca_tools.dir/correlate.cc.o
CMakeFiles/votca_tools.dir/crosscorrelate.cc.o
CMakeFiles/votca_tools.dir/cubicspline.cc.o
CMakeFiles/votca_tools.dir/datacollection.cc.o
CMakeFiles/votca_tools.dir/globals.cc.o
CMakeFiles/votca_tools.dir/histogram.cc.o
CMakeFiles/votca_tools.dir/histogramnew.cc.o
CMakeFiles/votca_tools.dir/linspline.cc.o
CMakeFiles/votca_tools.dir/matrix.cc.o
CMakeFiles/votca_tools.dir/mutex.cc.o
CMakeFiles/votca_tools.dir/parcer.cc.o
CMakeFiles/votca_tools.dir/parsexml.cc.o
CMakeFiles/votca_tools.dir/property.cc.o
CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o
CMakeFiles/votca_tools.dir/random.cc.o
CMakeFiles/votca_tools.dir/random2.cc.o
CMakeFiles/votca_tools.dir/rangeparser.cc.o
CMakeFiles/votca_tools.dir/spline.cc.o
CMakeFiles/votca_tools.dir/table.cc.o
CMakeFiles/votca_tools.dir/thread.cc.o
CMakeFiles/votca_tools.dir/tokenizer.cc.o
CMakeFiles/votca_tools.dir/version.cc.o
CMakeFiles/votca_tools.dir/linalg/gsl/cholesky.cc.o
CMakeFiles/votca_tools.dir/linalg/gsl/eigensystems.cc.o
CMakeFiles/votca_tools.dir/linalg/gsl/invert.cc.o
CMakeFiles/votca_tools.dir/linalg/gsl/qrsolve.cc.o
CMakeFiles/votca_tools.dir/linalg/gsl/svd.cc.o
/usr/local/boost/lib/libboost_program_options.dylib
/usr/local/boost/lib/libboost_filesystem.dylib
/usr/local/boost/lib/libboost_system.dylib /usr/local/gsl/lib/libgsl.dylib
/usr/local/fftw/lib/libfftw3.dylib /usr/lib/libexpat.dylib -lm
Undefined symbols for architecture x86_64:
"boost::program_options::to_internal(std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> > const&)",
referenced from:
std::__1::vector<std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> >,
std::__1::allocator<std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> > > >
boost::program_options::to_internal<std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> >
>(std::__1::vector<std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> >,
std::__1::allocator<std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> > > > const&) in
application.cc.o
"boost::program_options::options_description::options_description(std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned
int, unsigned int)", referenced from:
votca::tools::Application::Application() in application.cc.o
votca::tools::Application::AddProgramOptions(std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> > const&) in
application.cc.o
"boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::__1::pair<std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> >,
std::__1::basic_string<char, std::__1::char_traits<char>,
std::__1::allocator<char> > >, std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> > const&>)",
referenced from:
boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::__1::pair<std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> >,
std::__1::basic_string<char, std::__1::char_traits<char>,
std::__1::allocator<char> > >, std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> > const&>) in
application.cc.o
"boost::program_options::detail::cmdline::cmdline(std::__1::vector<std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> >,
std::__1::allocator<std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> > > > const&)",
referenced from:
boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int,
char const* const*) in application.cc.o
"boost::program_options::operator<<(std::__1::basic_ostream<char,
std::__1::char_traits<char> >&, boost::program_options::options_description
const&)", referenced from:
votca::tools::Application::ShowHelpText(std::__1::basic_ostream<char,
std::__1::char_traits<char> >&) in application.cc.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[2]: *** [src/libtools/libvotca_tools.3.dylib] Error 1
make[1]: *** [src/libtools/CMakeFiles/votca_tools.dir/all] Error 2
make: *** [all] Error 2
Google search hinted a possible cause of this error: both boost lib and the
project has to be linked against libstdc++, which is not the default case
with the newest clang compiler (by default now Apple replaced libstdc++
with libc++, but still keeps both of them for compatibility issues). I have
re-compiled boost lib and linked it with the current libstdc++ and tried
to pass -DCFLAGS="-stdlib=libstdc++" to the build.sh script, but still no
luck. Can be that libstdc++ is irrelevant to this error, but I've not found
any other reason.
Any ideas?
Best,
--Vitalie
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