Question: Problem to install Breakdancer on Mac OS X
1
gravatar for fbesnard
2.4 years ago by
fbesnard30
France
fbesnard30 wrote:

I am running Mac OS X 10.9.5.

I'm struggling to install Breakdancer.

I installed cmake (3.2.3) as required, with the command line option activated (symlink in my usr/bin/ folder)

I started Breakdancer compilation as recommended:

-1st step works fine ( cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local)

-but 2nd step (="make") fails :

Scanning dependencies of target boost-libs
[  1%] Creating directories for 'boost-libs'
[  3%] Performing download step (verify and extract) for 'boost-libs'

...

Scanning dependencies of target breakdancer
[ 43%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BedWriter.cpp.o
[ 45%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BreakDancer.cpp.o
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/breakdancer/BreakDancer.cpp:1:
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/breakdancer/BreakDancer.hpp:3:
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/breakdancer/BasicRegion.hpp:3:
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/io/Alignment.hpp:3:
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/common/ReadFlags.hpp:5:
/Users/lab/TOOLS_VariantAnalysis/breakdancer/build/vendor/boost/boost/include/boost/array.hpp:62:11: error:
      implicit instantiation of undefined template 'std::__1::basic_string<char,
      std::__1::char_traits<char>, std::__1::allocator<char> >'
        T elems[N];    // fixed-size array of elements of type T
          ^
/Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/common/ReadFlags.hpp:41:37: note:
      in instantiation of template class
      'boost::array<std::__1::basic_string<char, std::__1::char_traits<char>,
      std::__1::allocator<char> >, 11>' requested here
    PerFlagArray<std::string>::type strings_;
                                    ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/iosfwd:188:33: note:
      template is declared here
    class _LIBCPP_TYPE_VIS_ONLY basic_string;
                                ^
1 error generated.
make[2]: *** [build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BreakDancer.cpp.o] Error 1
make[1]: *** [build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/all] Error 2
make: *** [all] Error 2

Does anyone have a suggestion to solve this out ?

Fabrice

breakdancer mac os x • 1.5k views
ADD COMMENTlink modified 24 months ago by Biostar ♦♦ 20 • written 2.4 years ago by fbesnard30

No problem. I'd love to know if the changes worked for you or not. I hope they do!

ADD REPLYlink written 2.4 years ago by ernfrid180
1
gravatar for Ram
2.4 years ago by
Ram12k
New York
Ram12k wrote:

Try installing gcc4.9 through homebrew (gcc49) and use gcc49 (make CC=gcc49)as the compiler. Mac's gcc points to clang, which is stricter.

ADD COMMENTlink written 2.4 years ago by Ram12k

Hi Ram,

Thank you for feed back.

I installed gcc49 via MacPorts, and set it as the active compiler. Then I deleted my previous breakdancer folder and re-started all the installation from scratch, but it fails again at the same point (STEP=scanning dependencies of target breakdancer):

$make

Scanning dependencies of target boost-libs

[ 1%] Creating directories for 'boost-libs' ...

[ 36%] Performing configure step for 'gtest160'

-- The CXX compiler identification is GNU 4.9.2

-- The C compiler identification is GNU 4.9.2

-- Checking whether CXX compiler has -isysroot

-- Checking whether CXX compiler has -isysroot - yes

-- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes

-- Check for working CXX compiler: /opt/local/bin/c++

-- Check for working CXX compiler: /opt/local/bin/c++ -- works

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Checking whether C compiler has -isysroot

-- Checking whether C compiler has -isysroot - yes

-- Checking whether C compiler supports OSX deployment target flag

-- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /opt/local/bin/gcc

-- Check for working C compiler: /opt/local/bin/gcc

-- works -- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Detecting C compile features

-- Detecting C compile features - done

...

Scanning dependencies of target breakdancer

[ 43%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BedWriter.cpp.o

[ 45%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BreakDancer.cpp.o

In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/breakdancer/BreakDancer.cpp:1:

In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/breakdancer/BreakDancer.hpp:3:

In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/breakdancer/BasicRegion.hpp:3:

In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/io/Alignment.hpp:3:

In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/common/ReadFlags.hpp:5:

/Users/lab/TOOLS_VariantAnalysis/breakdancer/build/vendor/boost/boost/include/boost/array.hpp:62:11: error:

implicit instantiation of undefined template 'std::__1::basic_string, std::__1::allocator >' T elems[N]; // fixed-size array of elements of type T ^

/Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/common/ReadFlags.hpp:41:37: note: in instantiation of template class 'boost::array, std::__1::allocator >, 11>' requested here PerFlagArray::type strings_; ^

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/iosfwd:188:33: note: template is declared here class _LIBCPP_TYPE_VIS_ONLY basic_string; ^

1 error generated.

make[2]: *** [build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BreakDancer.cpp.o] Error 1

make[1]: *** [build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/all] Error 2

make: *** [all] Error 2

 

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by fbesnard30

I think the developers will be more suited to figure out the root cause. I ran this on my custom-configured-like-crazy Mac, and it gave me the same error. make deps then make, as suggested below by ernfrid, gives the same error as well.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Ram12k
1
gravatar for ernfrid
2.4 years ago by
ernfrid180
United States
ernfrid180 wrote:

I think the documentation on the install process may be slightly out of date. Can you please try the following? Rather than running make right off the bat, try running make deps and subsequently running make. Otherwise, leave everything the same.

ADD COMMENTlink written 2.4 years ago by ernfrid180

Hi Ernfrid,

 

I really believed it would work this time... but it ended up with the same crash.

namely, make deps  worked well but then  make failed at the same step again:

Scanning dependencies of target breakdancer

[ 43%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BedWriter.cpp.o

[ 45%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BreakDancer.cpp.o ... etc...

Is there something wrong with Xcode, since the last error message says:

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/iosfwd:188:33: note:

template is declared here class _LIBCPP_TYPE_VIS_ONLY basic_string;

But understanding this is way beyond my beginner's skills !

Fabrice

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by fbesnard30

I just pushed a commit to hopefully address this. I'm still getting compilation errors related to the testing library, but I do get a breakdancer-max executable after my change. Can you go ahead and give it a try now?

ADD REPLYlink written 2.4 years ago by ernfrid180

Hi Ernfrid,

Hey, there is improvement ! It is still failing, but it goes further in the compilation.

Again, It started it all from scratch, and I compile in 2 steps as you suggested before (make deps and then make)

1st step works fine, and during the 2nd:

-I get 1 warning at [63%]:

[ 63%] Building CXX object build/src/lib/io/CMakeFiles/io.dir/BamSummary.cpp.o
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/io/BamSummary.cpp:6:
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/io/BamIo.hpp:2:
/Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/io/BamReader.hpp:11:17: warning:
      function 'bamOpenMode' is not needed and will not be emitted
      [-Wunneeded-internal-declaration]
    char const* bamOpenMode(std::string const& path) {
                ^
1 warning generated.

-Then it crashes at [73%] during "Scanning dependencies of target breakdancer-max", generating a huge warning message:

[ 73%] Building CXX object build/src/exe/breakdancer-max/CMakeFiles/breakdancer-max.dir/BreakDancerMax.cpp.o
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/exe/breakdancer-max/BreakDancerMax.cpp:11:
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/io/BamIo.hpp:2:
/Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/io/BamReader.hpp:11:17: warning:
      function 'bamOpenMode' is not needed and will not be emitted
      [-Wunneeded-internal-declaration]
    char const* bamOpenMode(std::string const& path) {
                ^
1 warning generated.
Linking CXX executable ../../../../bin/breakdancer-max
Undefined symbols for architecture x86_64:
  "boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&)", referenced from:
      boost::archive::detail::iserializer<boost::archive::xml_iarchive, 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> > > >::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const in libio.a(ConfigLoader.cpp.o)
      boost::archive::detail::iserializer<boost::archive::xml_iarchive, std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long> >::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const in libio.a(ConfigLoader.cpp.o)
      boost::archive::detail::iserializer<boost::archive::xml_iarchive, std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned int> >::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const in libio.a(ConfigLoader.cpp.o)
      void LibraryConfig::serialize<boost::archive::xml_iarchive>(boost::archive::xml_iarchive&, unsigned int) in libio.a(ConfigLoader.cpp.o)
      void boost::serialization::stl::load_collection<boost::archive::xml_iarchive, 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::serialization::stl::archive_input_seq<boost::archive::xml_iarchive, 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::serialization::stl::reserve_imp<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::archive::xml_iarchive&, 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> > > >&) in libio.a(ConfigLoader.cpp.o)
      void boost::archive::detail::load_array_type<boost::archive::xml_iarchive>::invoke<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > [11]>(boost::archive::xml_iarchive&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > (&) [11]) in libio.a(ConfigLoader.cpp.o)
      void Options::serialize<boost::archive::xml_iarchive>(boost::archive::xml_iarchive&, unsigned int) in libio.a(ConfigLoader.cpp.o)
      ...
  "boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::xml_iarchive_impl(std::__1::basic_istream<char, std::__1::char_traits<char> >&, unsigned int)", referenced from:
      ConfigLoader::load_config(std::__1::basic_istream<char, std::__1::char_traits<char> >&) in libio.a(ConfigLoader.cpp.o)
  "boost::archive::xml_oarchive_impl<boost::archive::xml_oarchive>::save(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
      boost::archive::detail::oserializer<boost::archive::xml_oarchive, 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> > > > >::save_object_data(boost::archive::detail::basic_oarchive&, void const*) const in libio.a(ConfigLoader.cpp.o)
      boost::archive::detail::oserializer<boost::archive::xml_oarchive, 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> > > >::save_object_data(boost::archive::detail::basic_oarchive&, void const*) const in libio.a(ConfigLoader.cpp.o)
      boost::archive::detail::oserializer<boost::archive::xml_oarchive, std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long> >::save_object_data(boost::archive::detail::basic_oarchive&, void const*) const in libio.a(ConfigLoader.cpp.o)
      boost::archive::detail::oserializer<boost::archive::xml_oarchive, std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned int> >::save_object_data(boost::archive::detail::basic_oarchive&, void const*) const in libio.a(ConfigLoader.cpp.o)
      void LibraryConfig::serialize<boost::archive::xml_oarchive>(boost::archive::xml_oarchive&, unsigned int) in libio.a(ConfigLoader.cpp.o)
      void boost::archive::detail::save_array_type<boost::archive::xml_oarchive>::invoke<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > [11]>(boost::archive::xml_oarchive&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const (&) [11]) in libio.a(ConfigLoader.cpp.o)
      void Options::serialize<boost::archive::xml_oarchive>(boost::archive::xml_oarchive&, unsigned int) in libio.a(ConfigLoader.cpp.o)
      ...
  "boost::archive::xml_oarchive_impl<boost::archive::xml_oarchive>::xml_oarchive_impl(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, unsigned int)", referenced from:
      ConfigLoader::save_config(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in libio.a(ConfigLoader.cpp.o)
  "boost::archive::basic_text_oprimitive<std::__1::basic_ostream<char, std::__1::char_traits<char> > >::~basic_text_oprimitive()", referenced from:
      ConfigLoader::save_config(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in libio.a(ConfigLoader.cpp.o)
      boost::archive::xml_oarchive::~xml_oarchive() in libio.a(ConfigLoader.cpp.o)
      boost::archive::xml_oarchive::~xml_oarchive() in libio.a(ConfigLoader.cpp.o)
  "std::string::compare(char const*) const", referenced from:
      unsigned int boost::re_detail::find_sort_syntax<boost::re_detail::cpp_regex_traits_implementation<char>, char>(boost::re_detail::cpp_regex_traits_implementation<char> const*, char*) in libboost_regex.a(instances.o)
      char const* boost::re_detail::re_is_set_member<char const*, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(char const*, char const*, boost::re_detail::re_set_long<unsigned int> const*, boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool) in libboost_regex.a(instances.o)
      __gnu_cxx::__normal_iterator<char const*, std::string> boost::re_detail::re_is_set_member<__gnu_cxx::__normal_iterator<char const*, std::string>, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(__gnu_cxx::__normal_iterator<char const*, std::string>, __gnu_cxx::__normal_iterator<char const*, std::string>, boost::re_detail::re_set_long<unsigned int> const*, boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool) in libboost_regex.a(instances.o)
      char* boost::re_detail::re_is_set_member<char*, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(char*, char*, boost::re_detail::re_set_long<unsigned int> const*, boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool) in libboost_regex.a(instances.o)
      boost::re_detail::lookup_default_collate_name(std::string const&) in libboost_regex.a(regex_traits_defaults.o)
  "std::string::compare(std::string const&) const", referenced from:
      boost::re_detail::cpp_regex_traits_implementation<char>::lookup_classname_imp(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::init() in libboost_regex.a(instances.o)
      std::_Rb_tree<std::string, std::pair<std::string const, unsigned int>, std::_Select1st<std::pair<std::string const, unsigned int> >, std::less<std::string>, std::allocator<std::pair<std::string const, unsigned int> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<std::string const, unsigned int> >, std::pair<std::string const, unsigned int> const&) in libboost_regex.a(instances.o)
      boost::re_detail::basic_regex_creator<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::append_set(boost::re_detail::basic_char_set<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, mpl_::bool_<true>*) in libboost_regex.a(instances.o)
  "std::ctype<char>::_M_widen_init() const", referenced from:
      boost::re_detail::cpp_regex_traits_implementation<char>::init() in libboost_regex.a(instances.o)
      boost::archive::basic_text_oprimitive<std::ostream>::~basic_text_oprimitive() in libboost_serialization.a(basic_text_oprimitive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::~basic_text_oprimitive() in libboost_serialization.a(basic_text_oprimitive.o)
  "std::codecvt<char, char, __mbstate_t>::do_unshift(__mbstate_t&, char*, char*, char*&) const", referenced from:
      vtable for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_iprimitive.o)
      vtable for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_oprimitive.o)
  "std::codecvt<char, char, __mbstate_t>::do_encoding() const", referenced from:
      vtable for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_iprimitive.o)
      vtable for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_oprimitive.o)
  "std::codecvt<char, char, __mbstate_t>::do_max_length() const", referenced from:
      vtable for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_iprimitive.o)
      vtable for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_oprimitive.o)
  "std::codecvt<char, char, __mbstate_t>::do_in(__mbstate_t&, char const*, char const*, char const*&, char*, char*, char*&) const", referenced from:
      vtable for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_iprimitive.o)
      vtable for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_oprimitive.o)
  "std::codecvt<char, char, __mbstate_t>::do_out(__mbstate_t&, char const*, char const*, char const*&, char*, char*, char*&) const", referenced from:
      vtable for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_iprimitive.o)
      vtable for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_oprimitive.o)
  "std::codecvt<char, char, __mbstate_t>::do_length(__mbstate_t&, char const*, char const*, unsigned long) const", referenced from:
      vtable for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_iprimitive.o)
      vtable for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_oprimitive.o)
  "std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_Rep::_S_empty_rep_storage", referenced from:
      boost::archive::xml_iarchive_impl<boost::archive::naked_xml_iarchive>::load(std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&) in libboost_serialization.a(xml_iarchive.o)
  "std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::resize(unsigned long, wchar_t)", referenced from:
      boost::archive::xml_iarchive_impl<boost::archive::naked_xml_iarchive>::load(std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&) in libboost_serialization.a(xml_iarchive.o)
  "std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::reserve(unsigned long)", referenced from:
      boost::archive::xml_iarchive_impl<boost::archive::naked_xml_iarchive>::load(std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&) in libboost_serialization.a(xml_iarchive.o)
  "std::istream& std::istream::_M_extract<unsigned int>(unsigned int&)", referenced from:
      boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(boost::serialization::item_version_type&) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::naked_xml_iarchive>::load(boost::archive::version_type&) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::naked_xml_iarchive>::load(boost::serialization::item_version_type&) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(boost::archive::version_type&) in libboost_serialization.a(xml_iarchive.o)
  "std::istream& std::istream::_M_extract<unsigned short>(unsigned short&)", referenced from:
      boost::archive::basic_text_iprimitive<std::istream>::load(unsigned char&) in libboost_serialization.a(basic_text_iprimitive.o)
  "std::istream::get()", referenced from:
      boost::archive::basic_xml_grammar<char>::my_parse(std::istream&, boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> const&, char) const in libboost_serialization.a(xml_grammar.o)
      boost::archive::basic_text_iprimitive<std::istream>::load_binary(void*, unsigned long) in libboost_serialization.a(basic_text_iprimitive.o)
  "std::istream::peek()", referenced from:
      boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>, 8, 6, char>::fill() in libboost_serialization.a(basic_text_iprimitive.o)
  "std::istream::sync()", referenced from:
      boost::archive::basic_text_iprimitive<std::istream>::~basic_text_iprimitive() in libboost_serialization.a(basic_text_iprimitive.o)
      boost::archive::basic_text_iprimitive<std::istream>::~basic_text_iprimitive() in libboost_serialization.a(basic_text_iprimitive.o)
  "std::istream::ignore(long)", referenced from:
      boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>, 8, 6, char>::fill() in libboost_serialization.a(basic_text_iprimitive.o)
  "std::istream::putback(char)", referenced from:
      boost::archive::basic_xml_grammar<char>::parse_string(std::istream&, std::string&) in libboost_serialization.a(xml_grammar.o)
  "std::istream::operator>>(int&)", referenced from:
      boost::cpp_regex_traits<char>::toi(char const*&, char const*, int) const in libboost_regex.a(instances.o)
      boost::archive::basic_text_iprimitive<std::istream>::load(wchar_t&) in libboost_serialization.a(basic_text_iprimitive.o)
  "std::istream::operator>>(short&)", referenced from:
      boost::archive::basic_text_iprimitive<std::istream>::load(char&) in libboost_serialization.a(basic_text_iprimitive.o)
      boost::archive::basic_text_iprimitive<std::istream>::load(signed char&) in libboost_serialization.a(basic_text_iprimitive.o)
  "std::ostream::put(char)", referenced from:
      boost::archive::basic_xml_oarchive<boost::archive::xml_oarchive>::~basic_xml_oarchive() in libboost_serialization.a(xml_oarchive.o)
      boost::archive::basic_xml_oarchive<boost::archive::xml_oarchive>::~basic_xml_oarchive() in libboost_serialization.a(xml_oarchive.o)
      boost::archive::xml_oarchive_impl<boost::archive::xml_oarchive>::~xml_oarchive_impl() in libboost_serialization.a(xml_oarchive.o)
      boost::archive::xml_oarchive_impl<boost::archive::xml_oarchive>::~xml_oarchive_impl() in libboost_serialization.a(xml_oarchive.o)
      boost::archive::basic_xml_oarchive<boost::archive::xml_oarchive>::~basic_xml_oarchive() in libboost_serialization.a(xml_oarchive.o)
      boost::archive::xml_oarchive_impl<boost::archive::xml_oarchive>::save(char const*) in libboost_serialization.a(xml_oarchive.o)
      boost::archive::xml_oarchive_impl<boost::archive::xml_oarchive>::save(std::string const&) in libboost_serialization.a(xml_oarchive.o)
      ...
  "std::ostream::flush()", referenced from:
      boost::archive::basic_text_oprimitive<std::ostream>::~basic_text_oprimitive() in libboost_serialization.a(basic_text_oprimitive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::~basic_text_oprimitive() in libboost_serialization.a(basic_text_oprimitive.o)
  "std::ostream& std::ostream::_M_insert<bool>(bool)", referenced from:
      boost::archive::basic_text_oprimitive<std::ostream>::save(bool) in libboost_serialization.a(basic_text_oprimitive.o)
  "std::ostream& std::ostream::_M_insert<double>(double)", referenced from:
      boost::archive::basic_text_oprimitive<std::ostream>::save(float) in libboost_serialization.a(basic_text_oprimitive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::save(double) in libboost_serialization.a(basic_text_oprimitive.o)
  "std::ostream& std::ostream::_M_insert<unsigned long>(unsigned long)", referenced from:
      boost::archive::xml_oarchive_impl<boost::archive::xml_oarchive>::save(boost::serialization::item_version_type const&) in libboost_serialization.a(xml_oarchive.o)
      boost::archive::xml_oarchive_impl<boost::archive::xml_oarchive>::save(boost::archive::version_type const&) in libboost_serialization.a(xml_oarchive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::save(unsigned char) in libboost_serialization.a(basic_text_oprimitive.o)
  "std::ostream::operator<<(int)", referenced from:
      boost::archive::basic_xml_oarchive<boost::archive::xml_oarchive>::write_attribute(char const*, int, char const*) in libboost_serialization.a(xml_oarchive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::save(wchar_t) in libboost_serialization.a(basic_text_oprimitive.o)
  "std::ostream::operator<<(short)", referenced from:
      boost::archive::basic_text_oprimitive<std::ostream>::save(signed char) in libboost_serialization.a(basic_text_oprimitive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::save(char) in libboost_serialization.a(basic_text_oprimitive.o)
  "std::string::_M_leak_hard()", referenced from:
      boost::archive::basic_xml_iarchive<boost::archive::naked_xml_iarchive>::load_end(char const*) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::basic_xml_iarchive<boost::archive::xml_iarchive>::load_end(char const*) in libboost_serialization.a(xml_iarchive.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::lookup_collatename(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::init() in libboost_regex.a(instances.o)
      unsigned int boost::re_detail::find_sort_syntax<boost::re_detail::cpp_regex_traits_implementation<char>, char>(boost::re_detail::cpp_regex_traits_implementation<char> const*, char*) in libboost_regex.a(instances.o)
      ...
  "std::string::_M_replace_aux(unsigned long, unsigned long, unsigned long, char)", referenced from:
      char const* boost::re_detail::re_is_set_member<char const*, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(char const*, char const*, boost::re_detail::re_set_long<unsigned int> const*, boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool) in libboost_regex.a(instances.o)
      __gnu_cxx::__normal_iterator<char const*, std::string> boost::re_detail::re_is_set_member<__gnu_cxx::__normal_iterator<char const*, std::string>, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(__gnu_cxx::__normal_iterator<char const*, std::string>, __gnu_cxx::__normal_iterator<char const*, std::string>, boost::re_detail::re_set_long<unsigned int> const*, boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool) in libboost_regex.a(instances.o)
      char* boost::re_detail::re_is_set_member<char*, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(char*, char*, boost::re_detail::re_set_long<unsigned int> const*, boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool) in libboost_regex.a(instances.o)
      boost::re_detail::basic_regex_creator<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::append_set(boost::re_detail::basic_char_set<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, mpl_::bool_<false>*) in libboost_regex.a(instances.o)
  "std::string::_Rep::_M_destroy(std::allocator<char> const&)", referenced from:
      boost::system::(anonymous namespace)::generic_error_category::message(int) const in libboost_system.a(error_code.o)
      boost::archive::xml_iarchive_impl<boost::archive::naked_xml_iarchive>::load(char*) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(char*) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::naked_xml_iarchive>::load(wchar_t*) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::naked_xml_iarchive>::load(std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(wchar_t*) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&) in libboost_serialization.a(xml_iarchive.o)
      ...
  "std::string::_Rep::_S_empty_rep_storage", referenced from:
      boost::system::(anonymous namespace)::generic_error_category::message(int) const in libboost_system.a(error_code.o)
      boost::archive::xml_iarchive_impl<boost::archive::naked_xml_iarchive>::load(char*) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(char*) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::naked_xml_iarchive>::load(wchar_t*) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::naked_xml_iarchive>::load(std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(wchar_t*) in libboost_serialization.a(xml_iarchive.o)
      boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&) in libboost_serialization.a(xml_iarchive.o)
      ...
  "std::string::_Rep::_S_create(unsigned long, unsigned long, std::allocator<char> const&)", referenced from:
      boost::re_detail::cpp_regex_traits_implementation<char>::lookup_collatename(char const*, char const*) const in libboost_regex.a(instances.o)
      char* std::string::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag) in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::lookup_classname(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::basic_regex_parser<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::fail(boost::regex_constants::error_type, long, std::string, long) in libboost_regex.a(instances.o)
  "std::string::append(char const*, unsigned long)", referenced from:
      boost::re_detail::basic_regex_parser<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::fail(boost::regex_constants::error_type, long, std::string, long) in libboost_regex.a(instances.o)
      boost::re_detail::basic_regex_parser<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::fail(boost::regex_constants::error_type, long, std::string const&) in libboost_regex.a(instances.o)
  "std::string::append(std::string const&)", referenced from:
      boost::re_detail::cpp_regex_traits_implementation<char>::init() in libboost_regex.a(instances.o)
      boost::re_detail::basic_regex_parser<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::fail(boost::regex_constants::error_type, long, std::string, long) in libboost_regex.a(instances.o)
      boost::re_detail::basic_regex_parser<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::fail(boost::regex_constants::error_type, long, std::string const&) in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_char_layer<char>::init() in libboost_regex.a(cpp_regex_traits.o)
  "std::string::append(unsigned long, char)", referenced from:
      boost::re_detail::cpp_regex_traits_implementation<char>::init() in libboost_regex.a(instances.o)
  "std::string::assign(char const*, unsigned long)", referenced from:
      boost::system::(anonymous namespace)::generic_error_category::message(int) const in libboost_system.a(error_code.o)
  "std::string::assign(std::string const&)", referenced from:
      boost::re_detail::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::cpp_regex_traits<char>::catalog_name(std::string const&) in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::lookup_collatename(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::init() in libboost_regex.a(instances.o)
      char const* boost::re_detail::re_is_set_member<char const*, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(char const*, char const*, boost::re_detail::re_set_long<unsigned int> const*, boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool) in libboost_regex.a(instances.o)
      __gnu_cxx::__normal_iterator<char const*, std::string> boost::re_detail::re_is_set_member<__gnu_cxx::__normal_iterator<char const*, std::string>, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(__gnu_cxx::__normal_iterator<char const*, std::string>, __gnu_cxx::__normal_iterator<char const*, std::string>, boost::re_detail::re_set_long<unsigned int> const*, boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool) in libboost_regex.a(instances.o)
      ...
  "std::string::resize(unsigned long, char)", referenced from:
      boost::archive::basic_xml_grammar<char>::parse_start_tag(std::istream&) in libboost_serialization.a(xml_grammar.o)
      boost::archive::basic_xml_grammar<char>::parse_string(std::istream&, std::string&) in libboost_serialization.a(xml_grammar.o)
      boost::spirit::classic::impl::concrete_parser<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::strlit<wchar_t const*>, boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> >, boost::spirit::classic::chlit<wchar_t> >, boost::spirit::classic::action<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t>, boost::archive::xml::assign_impl<std::string> > >, boost::spirit::classic::chlit<wchar_t> >, boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t>::do_parse_virtual(boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> > const&) const in libboost_serialization.a(xml_grammar.o)
      boost::spirit::classic::impl::concrete_parser<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::optional<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> >, boost::spirit::classic::chlit<char> >, boost::spirit::classic::action<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t>, boost::archive::xml::assign_impl<std::string> > >, boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> >, boost::spirit::classic::optional<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> > >, boost::spirit::classic::chlit<char> >, boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t>::do_parse_virtual(boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> > const&) const in libboost_serialization.a(xml_grammar.o)
      boost::spirit::classic::impl::concrete_parser<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::optional<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> >, boost::spirit::classic::strlit<char const*> >, boost::spirit::classic::action<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t>, boost::archive::xml::assign_impl<std::string> > >, boost::spirit::classic::optional<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> > >, boost::spirit::classic::chlit<char> >, boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t>::do_parse_virtual(boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> > const&) const in libboost_serialization.a(xml_grammar.o)
  "std::string::replace(unsigned long, unsigned long, char const*, unsigned long)", referenced from:
      boost::re_detail::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::spirit::classic::impl::concrete_parser<boost::spirit::classic::action<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t>, boost::archive::xml::append_string<std::string, __gnu_cxx::__normal_iterator<char const*, std::string> > >, boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t>::do_parse_virtual(boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> > const&) const in libboost_serialization.a(xml_grammar.o)
  "std::string::reserve(unsigned long)", referenced from:
      boost::archive::basic_xml_grammar<char>::my_parse(std::istream&, boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> const&, char) const in libboost_serialization.a(xml_grammar.o)
      boost::spirit::classic::impl::concrete_parser<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::strlit<wchar_t const*>, boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> >, boost::spirit::classic::chlit<wchar_t> >, boost::spirit::classic::action<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t>, boost::archive::xml::assign_impl<std::string> > >, boost::spirit::classic::chlit<wchar_t> >, boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t>::do_parse_virtual(boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> > const&) const in libboost_serialization.a(xml_grammar.o)
      boost::spirit::classic::impl::concrete_parser<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::optional<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> >, boost::spirit::classic::chlit<char> >, boost::spirit::classic::action<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t>, boost::archive::xml::assign_impl<std::string> > >, boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> >, boost::spirit::classic::optional<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> > >, boost::spirit::classic::chlit<char> >, boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t>::do_parse_virtual(boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> > const&) const in libboost_serialization.a(xml_grammar.o)
      boost::spirit::classic::impl::concrete_parser<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::optional<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> >, boost::spirit::classic::strlit<char const*> >, boost::spirit::classic::action<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t>, boost::archive::xml::assign_impl<std::string> > >, boost::spirit::classic::optional<boost::spirit::classic::rule<boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t, boost::spirit::classic::nil_t> > >, boost::spirit::classic::chlit<char> >, boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t>::do_parse_virtual(boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> > const&) const in libboost_serialization.a(xml_grammar.o)
      boost::spirit::classic::impl::concrete_parser<boost::spirit::classic::action<boost::spirit::classic::strlit<wchar_t const*>, boost::archive::xml::append_lit<std::string, 38u> >, boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t>::do_parse_virtual(boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> > const&) const in libboost_serialization.a(xml_grammar.o)
      boost::spirit::classic::impl::concrete_parser<boost::spirit::classic::action<boost::spirit::classic::strlit<wchar_t const*>, boost::archive::xml::append_lit<std::string, 34u> >, boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t>::do_parse_virtual(boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> > const&) const in libboost_serialization.a(xml_grammar.o)
      boost::spirit::classic::impl::concrete_parser<boost::spirit::classic::action<boost::spirit::classic::strlit<wchar_t const*>, boost::archive::xml::append_lit<std::string, 39u> >, boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t>::do_parse_virtual(boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> > const&) const in libboost_serialization.a(xml_grammar.o)
      ...
  "std::string::_M_mutate(unsigned long, unsigned long, unsigned long)", referenced from:
      boost::re_detail::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const in libboost_regex.a(instances.o)
  "std::string::push_back(char)", referenced from:
      boost::spirit::classic::impl::concrete_parser<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::strlit<wchar_t const*>, boost::spirit::classic::action<boost::spirit::classic::uint_parser<unsigned int, 16, 1u, -1>, boost::archive::xml::append_char<std::string> > >, boost::spirit::classic::chlit<wchar_t> >, boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t>::do_parse_virtual(boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> > const&) const in libboost_serialization.a(xml_grammar.o)
      boost::spirit::classic::impl::concrete_parser<boost::spirit::classic::sequence<boost::spirit::classic::sequence<boost::spirit::classic::strlit<wchar_t const*>, boost::spirit::classic::action<boost::spirit::classic::uint_parser<unsigned int, 10, 1u, -1>, boost::archive::xml::append_char<std::string> > >, boost::spirit::classic::chlit<wchar_t> >, boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> >, boost::spirit::classic::nil_t>::do_parse_virtual(boost::spirit::classic::scanner<__gnu_cxx::__normal_iterator<char*, std::string>, boost::spirit::classic::scanner_policies<boost::spirit::classic::iteration_policy, boost::spirit::classic::match_policy, boost::spirit::classic::action_policy> > const&) const in libboost_serialization.a(xml_grammar.o)
  "std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)", referenced from:
      boost::system::(anonymous namespace)::generic_error_category::message(int) const in libboost_system.a(error_code.o)
      boost::re_detail::perl_matcher<char const*, std::allocator<boost::sub_match<char const*> >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags) in libboost_regex.a(instances.o)
      boost::re_detail::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::string>, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags) in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::init() in libboost_regex.a(instances.o)
      boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::imbue(std::locale) in libboost_regex.a(instances.o)
      boost::re_detail::basic_regex_creator<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::create_startmap(boost::re_detail::re_syntax_base*, unsigned char*, unsigned int*, unsigned char) (.constprop.651) in libboost_regex.a(instances.o)
      boost::match_results<char const*, std::allocator<boost::sub_match<char const*> > >::raise_logic_error() in libboost_regex.a(instances.o)
      ...
  "std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&)", referenced from:
      boost::system::(anonymous namespace)::generic_error_category::message(int) const in libboost_system.a(error_code.o)
      boost::cpp_regex_traits<char>::catalog_name(std::string const&) in libboost_regex.a(instances.o)
      boost::cpp_regex_traits<char>::get_catalog_name() in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::lookup_collatename(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::init() in libboost_regex.a(instances.o)
      boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::runtime_error> >::rethrow() const in libboost_regex.a(instances.o)
      boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::logic_error> >::rethrow() const in libboost_regex.a(instances.o)
      ...
  "std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(unsigned long, char, std::allocator<char> const&)", referenced from:
      boost::re_detail::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::lookup_collatename(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::basic_regex_creator<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::append_set(boost::re_detail::basic_char_set<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, mpl_::bool_<false>*) in libboost_regex.a(instances.o)
      boost::re_detail::lookup_default_collate_name(std::string const&) in libboost_regex.a(regex_traits_defaults.o)
  "std::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string()", referenced from:
      boost::system::(anonymous namespace)::generic_error_category::message(int) const in libboost_system.a(error_code.o)
      boost::cpp_regex_traits<char>::catalog_name(std::string const&) in libboost_regex.a(instances.o)
      boost::cpp_regex_traits<char>::get_catalog_name_inst() in libboost_regex.a(instances.o)
      boost::cpp_regex_traits<char>::get_catalog_name() in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::init() in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_char_layer<char>::init() in libboost_regex.a(cpp_regex_traits.o)
  "std::logic_error::logic_error(std::string const&)", referenced from:
      boost::match_results<char const*, std::allocator<boost::sub_match<char const*> > >::raise_logic_error() in libboost_regex.a(instances.o)
      boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::string>, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> > > >::raise_logic_error() in libboost_regex.a(instances.o)
      boost::re_detail::verify_options(unsigned int, boost::regex_constants::_match_flags) in libboost_regex.a(regex.o)
  "std::runtime_error::runtime_error(std::string const&)", referenced from:
      boost::re_detail::cpp_regex_traits_implementation<char>::init() in libboost_regex.a(instances.o)
      boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::imbue(std::locale) in libboost_regex.a(instances.o)
      void boost::re_detail::raise_error<boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > >(boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::error_type) in libboost_regex.a(instances.o)
      boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::regex_data() in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_char_layer<char>::init() in libboost_regex.a(cpp_regex_traits.o)
  "std::runtime_error::runtime_error(std::string const&)", referenced from:
      boost::regex_error::regex_error(std::string const&, boost::regex_constants::error_type, long) in libboost_regex.a(regex.o)
      boost::regex_error::regex_error(std::string const&, boost::regex_constants::error_type, long) in libboost_regex.a(regex.o)
      boost::regex_error::regex_error(boost::regex_constants::error_type) in libboost_regex.a(regex.o)
      boost::regex_error::regex_error(boost::regex_constants::error_type) in libboost_regex.a(regex.o)
  "std::basic_streambuf<char, std::char_traits<char> >::sync()", referenced from:
      vtable for boost::re_detail::parser_buf<char, std::char_traits<char> > in libboost_regex.a(instances.o)
  "std::basic_streambuf<char, std::char_traits<char> >::imbue(std::locale const&)", referenced from:
      vtable for boost::re_detail::parser_buf<char, std::char_traits<char> > in libboost_regex.a(instances.o)
  "std::basic_streambuf<char, std::char_traits<char> >::uflow()", referenced from:
      vtable for boost::re_detail::parser_buf<char, std::char_traits<char> > in libboost_regex.a(instances.o)
  "std::basic_streambuf<char, std::char_traits<char> >::xsgetn(char*, long)", referenced from:
      vtable for boost::re_detail::parser_buf<char, std::char_traits<char> > in libboost_regex.a(instances.o)
  "std::basic_streambuf<char, std::char_traits<char> >::xsputn(char const*, long)", referenced from:
      vtable for boost::re_detail::parser_buf<char, std::char_traits<char> > in libboost_regex.a(instances.o)
  "std::basic_streambuf<char, std::char_traits<char> >::overflow(int)", referenced from:
      vtable for boost::re_detail::parser_buf<char, std::char_traits<char> > in libboost_regex.a(instances.o)
  "std::basic_streambuf<char, std::char_traits<char> >::pbackfail(int)", referenced from:
      vtable for boost::re_detail::parser_buf<char, std::char_traits<char> > in libboost_regex.a(instances.o)
  "std::basic_streambuf<char, std::char_traits<char> >::showmanyc()", referenced from:
      vtable for boost::re_detail::parser_buf<char, std::char_traits<char> > in libboost_regex.a(instances.o)
  "std::basic_streambuf<char, std::char_traits<char> >::underflow()", referenced from:
      vtable for boost::re_detail::parser_buf<char, std::char_traits<char> > in libboost_regex.a(instances.o)
  "std::invalid_argument::invalid_argument(std::string const&)", referenced from:
      boost::re_detail::perl_matcher<char const*, std::allocator<boost::sub_match<char const*> >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags) in libboost_regex.a(instances.o)
      boost::re_detail::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::string>, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags) in libboost_regex.a(instances.o)
  "std::locale::_Impl::_M_install_facet(std::locale::id const*, std::locale::facet const*)", referenced from:
      std::locale::locale<boost::archive::codecvt_null<char> >(std::locale const&, boost::archive::codecvt_null<char>*) in libboost_serialization.a(basic_text_iprimitive.o)
      std::locale::locale<boost::archive::codecvt_null<char> >(std::locale const&, boost::archive::codecvt_null<char>*) in libboost_serialization.a(basic_text_oprimitive.o)
  "std::locale::_Impl::_Impl(std::locale::_Impl const&, unsigned long)", referenced from:
      std::locale::locale<boost::archive::codecvt_null<char> >(std::locale const&, boost::archive::codecvt_null<char>*) in libboost_serialization.a(basic_text_iprimitive.o)
      std::locale::locale<boost::archive::codecvt_null<char> >(std::locale const&, boost::archive::codecvt_null<char>*) in libboost_serialization.a(basic_text_oprimitive.o)
  "std::locale::_Impl::~_Impl()", referenced from:
      std::locale::locale<boost::archive::codecvt_null<char> >(std::locale const&, boost::archive::codecvt_null<char>*) in libboost_serialization.a(basic_text_iprimitive.o)
      std::locale::locale<boost::archive::codecvt_null<char> >(std::locale const&, boost::archive::codecvt_null<char>*) in libboost_serialization.a(basic_text_oprimitive.o)
  "std::locale::classic()", referenced from:
      boost::archive::basic_text_iprimitive<std::istream>::basic_text_iprimitive(std::istream&, bool) in libboost_serialization.a(basic_text_iprimitive.o)
      boost::archive::basic_text_iprimitive<std::istream>::basic_text_iprimitive(std::istream&, bool) in libboost_serialization.a(basic_text_iprimitive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::basic_text_oprimitive(std::ostream&, bool) in libboost_serialization.a(basic_text_oprimitive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::basic_text_oprimitive(std::ostream&, bool) in libboost_serialization.a(basic_text_oprimitive.o)
  "std::locale::locale(std::locale const&)", referenced from:
      boost::re_detail::cpp_regex_traits_base<char>::imbue(std::locale const&) in libboost_regex.a(instances.o)
      boost::cpp_regex_traits<char>::toi(char const*&, char const*, int) const in libboost_regex.a(instances.o)
      boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::imbue(std::locale) in libboost_regex.a(instances.o)
      std::_Rb_tree<boost::re_detail::cpp_regex_traits_base<char>, std::pair<boost::re_detail::cpp_regex_traits_base<char> const, std::_List_iterator<std::pair<boost::shared_ptr<boost::re_detail::cpp_regex_traits_implementation<char> const>, boost::re_detail::cpp_regex_traits_base<char> const*> > >, std::_Select1st<std::pair<boost::re_detail::cpp_regex_traits_base<char> const, std::_List_iterator<std::pair<boost::shared_ptr<boost::re_detail::cpp_regex_traits_implementation<char> const>, boost::re_detail::cpp_regex_traits_base<char> const*> > > >, std::less<boost::re_detail::cpp_regex_traits_base<char> >, std::allocator<std::pair<boost::re_detail::cpp_regex_traits_base<char> const, std::_List_iterator<std::pair<boost::shared_ptr<boost::re_detail::cpp_regex_traits_implementation<char> const>, boost::re_detail::cpp_regex_traits_base<char> const*> > > > >::_M_insert_unique(std::pair<boost::re_detail::cpp_regex_traits_base<char> const, std::_List_iterator<std::pair<boost::shared_ptr<boost::re_detail::cpp_regex_traits_implementation<char> const>, boost::re_detail::cpp_regex_traits_base<char> const*> > > const&) in libboost_regex.a(instances.o)
      boost::object_cache<boost::re_detail::cpp_regex_traits_base<char>, boost::re_detail::cpp_regex_traits_implementation<char> >::do_get(boost::re_detail::cpp_regex_traits_base<char> const&, unsigned long) in libboost_regex.a(instances.o)
      boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::regex_data() in libboost_regex.a(instances.o)
      boost::archive::basic_text_iprimitive<std::istream>::~basic_text_iprimitive() in libboost_serialization.a(basic_text_iprimitive.o)
      ...
  "std::locale::locale()", referenced from:
      boost::cpp_regex_traits<char>::toi(char const*&, char const*, int) const in libboost_regex.a(instances.o)
      boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::imbue(std::locale) in libboost_regex.a(instances.o)
      boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::regex_data() in libboost_regex.a(instances.o)
  "std::locale::~locale()", referenced from:
      boost::re_detail::cpp_regex_traits_base<char>::imbue(std::locale const&) in libboost_regex.a(instances.o)
      boost::cpp_regex_traits<char>::toi(char const*&, char const*, int) const in libboost_regex.a(instances.o)
      boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::imbue(std::locale) in libboost_regex.a(instances.o)
      boost::re_detail::parser_buf<char, std::char_traits<char> >::~parser_buf() in libboost_regex.a(instances.o)
      boost::re_detail::parser_buf<char, std::char_traits<char> >::~parser_buf() in libboost_regex.a(instances.o)
      std::_Rb_tree<boost::re_detail::cpp_regex_traits_base<char>, std::pair<boost::re_detail::cpp_regex_traits_base<char> const, std::_List_iterator<std::pair<boost::shared_ptr<boost::re_detail::cpp_regex_traits_implementation<char> const>, boost::re_detail::cpp_regex_traits_base<char> const*> > >, std::_Select1st<std::pair<boost::re_detail::cpp_regex_traits_base<char> const, std::_List_iterator<std::pair<boost::shared_ptr<boost::re_detail::cpp_regex_traits_implementation<char> const>, boost::re_detail::cpp_regex_traits_base<char> const*> > > >, std::less<boost::re_detail::cpp_regex_traits_base<char> >, std::allocator<std::pair<boost::re_detail::cpp_regex_traits_base<char> const, std::_List_iterator<std::pair<boost::shared_ptr<boost::re_detail::cpp_regex_traits_implementation<char> const>, boost::re_detail::cpp_regex_traits_base<char> const*> > > > >::_M_erase(std::_Rb_tree_node<std::pair<boost::re_detail::cpp_regex_traits_base<char> const, std::_List_iterator<std::pair<boost::shared_ptr<boost::re_detail::cpp_regex_traits_implementation<char> const>, boost::re_detail::cpp_regex_traits_base<char> const*> > > >*) in libboost_regex.a(instances.o)
      boost::detail::sp_counted_impl_p<boost::re_detail::cpp_regex_traits_implementation<char> >::dispose() in libboost_regex.a(instances.o)
      ...
  "std::locale::operator=(std::locale const&)", referenced from:
      boost::re_detail::cpp_regex_traits_base<char>::imbue(std::locale const&) in libboost_regex.a(instances.o)
      boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::imbue(std::locale) in libboost_regex.a(instances.o)
      boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::regex_data() in libboost_regex.a(instances.o)
      boost::archive::basic_text_iprimitive<std::istream>::~basic_text_iprimitive() in libboost_serialization.a(basic_text_iprimitive.o)
      boost::archive::basic_text_iprimitive<std::istream>::~basic_text_iprimitive() in libboost_serialization.a(basic_text_iprimitive.o)
      boost::archive::basic_streambuf_locale_saver<char, std::char_traits<char> >::~basic_streambuf_locale_saver() in libboost_serialization.a(basic_text_iprimitive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::~basic_text_oprimitive() in libboost_serialization.a(basic_text_oprimitive.o)
      ...
  "std::codecvt<char, char, __mbstate_t>::id", referenced from:
      std::locale::locale<boost::archive::codecvt_null<char> >(std::locale const&, boost::archive::codecvt_null<char>*) in libboost_serialization.a(basic_text_iprimitive.o)
      std::locale::locale<boost::archive::codecvt_null<char> >(std::locale const&, boost::archive::codecvt_null<char>*) in libboost_serialization.a(basic_text_oprimitive.o)
  "std::codecvt<char, char, __mbstate_t>::codecvt(unsigned long)", referenced from:
      boost::archive::basic_text_iprimitive<std::istream>::basic_text_iprimitive(std::istream&, bool) in libboost_serialization.a(basic_text_iprimitive.o)
      boost::archive::basic_text_iprimitive<std::istream>::basic_text_iprimitive(std::istream&, bool) in libboost_serialization.a(basic_text_iprimitive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::basic_text_oprimitive(std::ostream&, bool) in libboost_serialization.a(basic_text_oprimitive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::basic_text_oprimitive(std::ostream&, bool) in libboost_serialization.a(basic_text_oprimitive.o)
  "std::codecvt<char, char, __mbstate_t>::~codecvt()", referenced from:
      boost::archive::codecvt_null<char>::~codecvt_null() in libboost_serialization.a(basic_text_iprimitive.o)
      boost::archive::codecvt_null<char>::~codecvt_null() in libboost_serialization.a(basic_text_iprimitive.o)
      boost::archive::codecvt_null<char>::~codecvt_null() in libboost_serialization.a(basic_text_oprimitive.o)
      boost::archive::codecvt_null<char>::~codecvt_null() in libboost_serialization.a(basic_text_oprimitive.o)
  "std::__detail::_List_node_base::_M_transfer(std::__detail::_List_node_base*, std::__detail::_List_node_base*)", referenced from:
      boost::object_cache<boost::re_detail::cpp_regex_traits_base<char>, boost::re_detail::cpp_regex_traits_implementation<char> >::do_get(boost::re_detail::cpp_regex_traits_base<char> const&, unsigned long) in libboost_regex.a(instances.o)
  "std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)", referenced from:
      boost::archive::detail::shared_ptr_helper::append(boost_132::shared_ptr<void const> const&) in libboost_serialization.a(shared_ptr_helper.o)
      boost::object_cache<boost::re_detail::cpp_regex_traits_base<char>, boost::re_detail::cpp_regex_traits_implementation<char> >::do_get(boost::re_detail::cpp_regex_traits_base<char> const&, unsigned long) in libboost_regex.a(instances.o)
  "std::__detail::_List_node_base::_M_unhook()", referenced from:
      boost::object_cache<boost::re_detail::cpp_regex_traits_base<char>, boost::re_detail::cpp_regex_traits_implementation<char> >::do_get(boost::re_detail::cpp_regex_traits_base<char> const&, unsigned long) in libboost_regex.a(instances.o)
  "std::ios_base::Init::Init()", referenced from:
      __GLOBAL__sub_I_xml_iarchive.cpp in libboost_serialization.a(xml_iarchive.o)
      __GLOBAL__sub_I_xml_oarchive.cpp in libboost_serialization.a(xml_oarchive.o)
  "std::ios_base::Init::~Init()", referenced from:
      __GLOBAL__sub_I_xml_iarchive.cpp in libboost_serialization.a(xml_iarchive.o)
      __GLOBAL__sub_I_xml_oarchive.cpp in libboost_serialization.a(xml_oarchive.o)
  "std::ios_base::ios_base()", referenced from:
      boost::cpp_regex_traits<char>::toi(char const*&, char const*, int) const in libboost_regex.a(instances.o)
  "std::ios_base::~ios_base()", referenced from:
      boost::cpp_regex_traits<char>::toi(char const*&, char const*, int) const in libboost_regex.a(instances.o)
  "std::basic_ios<char, std::char_traits<char> >::init(std::basic_streambuf<char, std::char_traits<char> >*)", referenced from:
      boost::cpp_regex_traits<char>::toi(char const*&, char const*, int) const in libboost_regex.a(instances.o)
  "std::basic_ios<char, std::char_traits<char> >::clear(std::_Ios_Iostate)", referenced from:
      boost::cpp_regex_traits<char>::toi(char const*&, char const*, int) const in libboost_regex.a(instances.o)
  "std::basic_ios<char, std::char_traits<char> >::imbue(std::locale const&)", referenced from:
      boost::archive::basic_text_iprimitive<std::istream>::basic_text_iprimitive(std::istream&, bool) in libboost_serialization.a(basic_text_iprimitive.o)
      boost::archive::basic_text_iprimitive<std::istream>::basic_text_iprimitive(std::istream&, bool) in libboost_serialization.a(basic_text_iprimitive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::basic_text_oprimitive(std::ostream&, bool) in libboost_serialization.a(basic_text_oprimitive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::basic_text_oprimitive(std::ostream&, bool) in libboost_serialization.a(basic_text_oprimitive.o)
  "std::__throw_bad_cast()", referenced from:
      boost::archive::basic_text_oprimitive<std::ostream>::~basic_text_oprimitive() in libboost_serialization.a(basic_text_oprimitive.o)
      boost::archive::basic_text_oprimitive<std::ostream>::~basic_text_oprimitive() in libboost_serialization.a(basic_text_oprimitive.o)
  "std::_Rb_tree_decrement(std::_Rb_tree_node_base*)", referenced from:
      boost::archive::detail::basic_iarchive::register_basic_serializer(boost::archive::detail::basic_iserializer const&) in libboost_serialization.a(basic_iarchive.o)
      boost::archive::detail::basic_iarchive::load_object(void*, boost::archive::detail::basic_iserializer const&) in libboost_serialization.a(basic_iarchive.o)
      boost::archive::detail::basic_iarchive_impl::load_pointer(boost::archive::detail::basic_iarchive&, void*&, boost::archive::detail::basic_pointer_iserializer const*, boost::archive::detail::basic_pointer_iserializer const* (*)(boost::serialization::extended_type_info const&)) in libboost_serialization.a(basic_iarchive.o)
      boost::archive::detail::basic_oarchive::register_basic_serializer(boost::archive::detail::basic_oserializer const&) in libboost_serialization.a(basic_oarchive.o)
      boost::archive::detail::basic_oarchive::save_object(void const*, boost::archive::detail::basic_oserializer const&) in libboost_serialization.a(basic_oarchive.o)
      boost::archive::detail::basic_oarchive::save_pointer(void const*, boost::archive::detail::basic_pointer_oserializer const*) in libboost_serialization.a(basic_oarchive.o)
      std::_Rb_tree<boost::archive::detail::basic_oarchive_impl::aobject, boost::archive::detail::basic_oarchive_impl::aobject, std::_Identity<boost::archive::detail::basic_oarchive_impl::aobject>, std::less<boost::archive::detail::basic_oarchive_impl::aobject>, std::allocator<boost::archive::detail::basic_oarchive_impl::aobject> >::_M_insert_unique(boost::archive::detail::basic_oarchive_impl::aobject const&) in libboost_serialization.a(basic_oarchive.o)
      ...
  "std::_Rb_tree_increment(std::_Rb_tree_node_base const*)", referenced from:
      boost::serialization::typeid_system::extended_type_info_typeid_0::type_unregister() in libboost_serialization.a(extended_type_info_typeid.o)
      boost::serialization::extended_type_info::key_unregister() const in libboost_serialization.a(extended_type_info.o)
      boost::object_cache<boost::re_detail::cpp_regex_traits_base<char>, boost::re_detail::cpp_regex_traits_implementation<char> >::do_get(boost::re_detail::cpp_regex_traits_base<char> const&, unsigned long) in libboost_regex.a(instances.o)
      boost::serialization::void_cast_detail::void_caster::recursive_unregister() const (.part.41) in libboost_serialization.a(void_cast.o)
      boost::serialization::void_cast_detail::void_caster_shortcut::vbc_upcast(void const*) const in libboost_serialization.a(void_cast.o)
      boost::serialization::void_cast_detail::void_caster_shortcut::vbc_downcast(void const*) const in libboost_serialization.a(void_cast.o)
      boost::serialization::void_cast_detail::void_caster::recursive_register(bool) const in libboost_serialization.a(void_cast.o)
      ...
  "std::_Rb_tree_increment(std::_Rb_tree_node_base*)", referenced from:
      std::_Rb_tree<int, std::pair<int const, std::string>, std::_Select1st<std::pair<int const, std::string> >, std::less<int>, std::allocator<std::pair<int const, std::string> > >::_M_get_insert_hint_unique_pos(std::_Rb_tree_const_iterator<std::pair<int const, std::string> >, int const&) in libboost_regex.a(instances.o)
      std::_Rb_tree<std::string, std::pair<std::string const, unsigned int>, std::_Select1st<std::pair<std::string const, unsigned int> >, std::less<std::string>, std::allocator<std::pair<std::string const, unsigned int> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<std::string const, unsigned int> >, std::pair<std::string const, unsigned int> const&) in libboost_regex.a(instances.o)
  "std::__throw_logic_error(char const*)", referenced from:
      char* std::string::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag) in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::lookup_classname(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::basic_regex_parser<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::fail(boost::regex_constants::error_type, long, std::string, long) in libboost_regex.a(instances.o)
  "std::__throw_length_error(char const*)", referenced from:
      std::vector<boost::sub_match<char const*>, std::allocator<boost::sub_match<char const*> > >::_M_fill_insert(__gnu_cxx::__normal_iterator<boost::sub_match<char const*>*, std::vector<boost::sub_match<char const*>, std::allocator<boost::sub_match<char const*> > > >, unsigned long, boost::sub_match<char const*> const&) in libboost_regex.a(instances.o)
      std::vector<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> > > >::_M_fill_insert(__gnu_cxx::__normal_iterator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> >*, std::vector<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> > > > >, unsigned long, boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::string> > const&) in libboost_regex.a(instances.o)
      std::vector<bool, std::allocator<bool> >::_M_fill_insert(std::_Bit_iterator, unsigned long, bool) in libboost_regex.a(instances.o)
  "std::__throw_out_of_range_fmt(char const*, ...)", referenced from:
      boost::re_detail::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const in libboost_regex.a(instances.o)
      boost::re_detail::basic_regex_parser<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::parse_perl_extension() in libboost_regex.a(instances.o)
      boost::re_detail::basic_regex_parser<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::parse_open_paren() in libboost_regex.a(instances.o)
      std::bitset<256ul>::_M_check(unsigned long, char const*) const (.isra.116.part.117) in libboost_serialization.a(xml_grammar.o)
  "std::_Rb_tree_rebalance_for_erase(std::_Rb_tree_node_base*, std::_Rb_tree_node_base&)", referenced from:
      boost::serialization::typeid_system::extended_type_info_typeid_0::type_unregister() in libboost_serialization.a(extended_type_info_typeid.o)
      boost::serialization::extended_type_info::key_unregister() const in libboost_serialization.a(extended_type_info.o)
      boost::object_cache<boost::re_detail::cpp_regex_traits_base<char>, boost::re_detail::cpp_regex_traits_implementation<char> >::do_get(boost::re_detail::cpp_regex_traits_base<char> const&, unsigned long) in libboost_regex.a(instances.o)
      boost::serialization::void_cast_detail::void_caster::recursive_unregister() const (.part.41) in libboost_serialization.a(void_cast.o)
      boost::archive::detail::basic_serializer_map::erase(boost::archive::detail::basic_serializer const*) in libboost_serialization.a(basic_serializer_map.o)
  "std::_Rb_tree_insert_and_rebalance(bool, std::_Rb_tree_node_base*, std::_Rb_tree_node_base*, std::_Rb_tree_node_base&)", referenced from:
      boost::serialization::typeid_system::extended_type_info_typeid_0::type_register(std::type_info const&) in libboost_serialization.a(extended_type_info_typeid.o)
      boost::archive::detail::basic_iarchive::register_basic_serializer(boost::archive::detail::basic_iserializer const&) in libboost_serialization.a(basic_iarchive.o)
      boost::archive::detail::basic_iarchive::load_object(void*, boost::archive::detail::basic_iserializer const&) in libboost_serialization.a(basic_iarchive.o)
      boost::archive::detail::basic_iarchive_impl::load_pointer(boost::archive::detail::basic_iarchive&, void*&, boost::archive::detail::basic_pointer_iserializer const*, boost::archive::detail::basic_pointer_iserializer const* (*)(boost::serialization::extended_type_info const&)) in libboost_serialization.a(basic_iarchive.o)
      boost::archive::detail::basic_oarchive::register_basic_serializer(boost::archive::detail::basic_oserializer const&) in libboost_serialization.a(basic_oarchive.o)
      boost::archive::detail::basic_oarchive::save_object(void const*, boost::archive::detail::basic_oserializer const&) in libboost_serialization.a(basic_oarchive.o)
      boost::archive::detail::basic_oarchive::save_pointer(void const*, boost::archive::detail::basic_pointer_oserializer const*) in libboost_serialization.a(basic_oarchive.o)
      ...
  "bool std::has_facet<std::messages<char> >(std::locale const&)", referenced from:
      boost::re_detail::cpp_regex_traits_base<char>::imbue(std::locale const&) in libboost_regex.a(instances.o)
      boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::imbue(std::locale) in libboost_regex.a(instances.o)
      boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::regex_data() in libboost_regex.a(instances.o)
  "std::ctype<char> const& std::use_facet<std::ctype<char> >(std::locale const&)", referenced from:
      boost::re_detail::cpp_regex_traits_base<char>::imbue(std::locale const&) in libboost_regex.a(instances.o)
      boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::imbue(std::locale) in libboost_regex.a(instances.o)
      boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::regex_data() in libboost_regex.a(instances.o)
  "std::collate<char> const& std::use_facet<std::collate<char> >(std::locale const&)", referenced from:
      boost::re_detail::cpp_regex_traits_base<char>::imbue(std::locale const&) in libboost_regex.a(instances.o)
      boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::imbue(std::locale) in libboost_regex.a(instances.o)
      boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::regex_data() in libboost_regex.a(instances.o)
  "std::messages<char> const& std::use_facet<std::messages<char> >(std::locale const&)", referenced from:
      boost::re_detail::cpp_regex_traits_base<char>::imbue(std::locale const&) in libboost_regex.a(instances.o)
      boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::imbue(std::locale) in libboost_regex.a(instances.o)
      boost::re_detail::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::regex_data() in libboost_regex.a(instances.o)
  "std::numpunct<char> const& std::use_facet<std::numpunct<char> >(std::locale const&)", referenced from:
      boost::cpp_regex_traits<char>::toi(char const*&, char const*, int) const in libboost_regex.a(instances.o)
  "typeinfo for std::basic_streambuf<char, std::char_traits<char> >", referenced from:
      typeinfo for boost::re_detail::parser_buf<char, std::char_traits<char> > in libboost_regex.a(instances.o)
  "typeinfo for std::codecvt<char, char, __mbstate_t>", referenced from:
      typeinfo for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_iprimitive.o)
      typeinfo for boost::archive::codecvt_null<char> in libboost_serialization.a(basic_text_oprimitive.o)
  "vtable for std::istream", referenced from:
      boost::cpp_regex_traits<char>::toi(char const*&, char const*, int) const in libboost_regex.a(instances.o)
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
  "vtable for std::basic_streambuf<char, std::char_traits<char> >", referenced from:
      boost::cpp_regex_traits<char>::toi(char const*&, char const*, int) const in libboost_regex.a(instances.o)
      boost::re_detail::parser_buf<char, std::char_traits<char> >::~parser_buf() in libboost_regex.a(instances.o)
      boost::re_detail::parser_buf<char, std::char_traits<char> >::~parser_buf() in libboost_regex.a(instances.o)
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
  "vtable for std::basic_ios<char, std::char_traits<char> >", referenced from:
      boost::cpp_regex_traits<char>::toi(char const*&, char const*, int) const in libboost_regex.a(instances.o)
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
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]: *** [bin/breakdancer-max] Error 1
make[1]: *** [build/src/exe/breakdancer-max/CMakeFiles/breakdancer-max.dir/all] Error 2
make: *** [all] Error 2

 

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by fbesnard30
1

Well that's confusing. I did not have this problem on my Mac, but I am running 10.10.3. I do wonder if the issue might be related to your earlier attempts to compile with GCC. The linker errors could be indicating that boost was compiled with GCC, but Breakdancer is being compiled with Clang. Did you remove all files from your build directory before trying to compile again? 

ADD REPLYlink written 2.4 years ago by ernfrid180

Hi

before each new trial, I remove the breakdancer folder (rm -rf breakdancer) and I re-download it from github (git clone --recursive https://github.com/genome/breakdancer.git).

Do you think I should do something else ? Are there other files created somewhere else that I should remove ?
 

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by fbesnard30

Nope, as long as you've removed the directory you were running make in you should be fine. Removing the whole breakdancer directory should definitely take care of it if you are following the directions. Have you tried Ram's earlier suggestion of using GCC as well? I'd make sure to use it for both make deps and make. If that doesn't work, I'll do some more research, but it will be difficult with me unable to replicate the issue. 

ADD REPLYlink written 2.4 years ago by ernfrid180

Hi Ernfrid,

Yes I installed gcc49 as suggested by Ram.

breakdancer was compiling using it, as said during the progress:

The CXX compiler identification is GNU 4.9.2

-- The C compiler identification is GNU 4.9.2

And when I type: gcc --version, I get:
gcc (MacPorts gcc49 4.9.2_2) 4.9.2
Copyright (C) 2014 Free Software Foundation, Inc.

Since I set it as the default compiler, it should be used both for make deps and make, right ?

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by fbesnard30

I'm not too sure. Certainly the end of your output indicates clang is what is running.

clang: error: linker command failed with exit code 1 (use -v to see invocation)

That is why I thought you were running clang and not gcc. I can't say why the output would indicate GNU 4.9.2 but then the error output is indicating clang.

I will look into installing GCC via macports on my machine as well and see if I can't replicate the issue in that manner. In the meantime, can you uninstall gcc via macports and try then?

ADD REPLYlink written 2.4 years ago by ernfrid180

Ok. I can confirm that installing gcc via macports, selecting gcc as the compiler via macports (sudo port select --set gcc mp-gcc49) and then compiling Breakdancer will fail. Cmake seems to think the compiler is still AppleClang, but later on in the build process, Breakdancer itself is being compiled with gcc4.9.

In my case, deselecting gcc as the compiler (sudo port select --set gcc none) resolves the immediate problem of a failed compilation. 

ADD REPLYlink written 2.4 years ago by ernfrid180

Hi fbesnard,

Were you able to get this to  work with the changes and recommendations I made?

ADD REPLYlink written 2.4 years ago by ernfrid180

Hi Ernfrid,

 

Excuse-me, I haven't tried yet: I had to pause this job to deal with others urgent things.

I drop you a reply as soon as I get back to this (next week I guess). Thank you very much for your help anyway, I really appreciate your feedback !

ADD REPLYlink written 2.4 years ago by fbesnard30
0
gravatar for fbesnard
2.1 years ago by
fbesnard30
France
fbesnard30 wrote:

Hi,

After a long pause, I'm getting back to this issue... without success.

I did what Ernfrid suggested, which is sudo port select --set gcc none.

To sum up, here is what I did after:

1)rm -rf breakdancer then git clone --recursive https://github.com/genome/breakdancer.git

2) Create "build" folder and in it, type:

cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local

3)As first suggested by Ernfrid, I install in two times by typing:

make deps (works well)

make, where it fails.

The compilation gets a little bit further than previously (75% instead of 73%), but still crashes:

Scanning dependencies of target TestBdLib
[ 75%] Building CXX object build/test/lib/breakdancer/CMakeFiles/TestBdLib.dir/TestBreakDancer.cpp.o
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/test/lib/breakdancer/TestBreakDancer.cpp:9:
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/build/vendor/src/gtest160/include/gtest/gtest.h:57:
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/build/vendor/src/gtest160/include/gtest/internal/gtest-internal.h:40:
/Users/lab/TOOLS_VariantAnalysis/breakdancer/build/vendor/src/gtest160/include/gtest/internal/gtest-port.h:499:13: fatal error:
      'tr1/tuple' file not found
#   include <tr1/tuple>  // NOLINT
            ^
1 error generated.
make[2]: *** [build/test/lib/breakdancer/CMakeFiles/TestBdLib.dir/TestBreakDancer.cpp.o] Error 1
make[1]: *** [build/test/lib/breakdancer/CMakeFiles/TestBdLib.dir/all] Error 2
make: *** [all] Error 2

 

Any ideas ??

Thank you,

 

Fabrice

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by fbesnard30

I never saw this update, but I did push a correction about a week ago that may fix your issue. Can you try it again?

ADD REPLYlink written 2.1 years ago by ernfrid180
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 593 users visited in the last hour