Moving on...
Now I get the message (see below). What's the difference?
In the Release-based link.txt we have:
-install_name
/Users/pemsley/autobuild/b-e-l/rdkit-Release_2015_03_1/build/lib/libSLNParse.1.dylib
In the git-based link.txt we have:
-install_name
@rpath/libSLNParse.1.dylib
Is that relevant?
libboost_regexp has the necessary functions:
$ nm
~/autobuild/build-coot+rdkit-pre-release-gtk2-python/lib/libboost_regex.dylib
| grep mem_block
0000000000053910 T __ZN5boost9re_detail13get_mem_blockEv
0000000000053990 T __ZN5boost9re_detail13put_mem_blockEPv
0000000000053ae0 t __ZN5boost9re_detail15mem_block_cacheD1Ev
I am not explicitly using -stdlib anywhere.
Paul.
---------------------------------------------------
$ make VERBOSE=1
[snip]
[ 84%] Linking CXX shared library ../../../lib/libSLNParse.dylib
cd
/Users/pemsley/autobuild/b-e-l/rdkit-github/build/Code/GraphMol/SLNParse
&& /sw/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt
--verbose=1
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC
-Wall -Wextra -O3 -DNDEBUG -dynamiclib -Wl,-headerpad_max_install_names
-compatibility_version 1.0.0 -current_version 2016.3.1 -o
../../../lib/libSLNParse.2016.03.1.dev1.dylib -install_name
@rpath/libSLNParse.1.dylib CMakeFiles/SLNParse.dir/SLNParse.cpp.o
CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o
CMakeFiles/SLNParse.dir/sln.tab.cpp.o
CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -L$install_prefix/lib
../../../lib/libGraphMol.2016.03.1.dev1.dylib
$install_prefix/lib/libboost_regex.dylib
../../../lib/libRDGeometryLib.2016.03.1.dev1.dylib
../../../lib/libDataStructs.2016.03.1.dev1.dylib
../../../lib/libRDGeneral.2016.03.1.dev1.dylib
-Wl,-rpath,/Users/pemsley/autobuild/b-e-l/rdkit-github/build/lib
-Wl,-rpath,$install_prefix/lib
Undefined symbols for architecture x86_64:
"boost::re_detail_106000::get_mem_block()", referenced from:
boost::re_detail_106000::perl_matcher<std::__1::__wrap_iter<char
const*>, std::__1::allocator<boost::sub_match<std::__1::__wrap_iter<char
const*> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> >
>::find_imp() in SLNParse.cpp.o
boost::re_detail_106000::perl_matcher<std::__1::__wrap_iter<char
const*>, std::__1::allocator<boost::sub_match<std::__1::__wrap_iter<char
const*> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> >
>::unwind_commit(bool) in SLNParse.cpp.o
boost::re_detail_106000::perl_matcher<std::__1::__wrap_iter<char
const*>, std::__1::allocator<boost::sub_match<std::__1::__wrap_iter<char
const*> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> >
>::match_all_states() in SLNParse.cpp.o
boost::re_detail_106000::perl_matcher<std::__1::__wrap_iter<char
const*>, std::__1::allocator<boost::sub_match<std::__1::__wrap_iter<char
const*> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> >
>::match_startmark() in SLNParse.cpp.o
boost::re_detail_106000::perl_matcher<std::__1::__wrap_iter<char
const*>, std::__1::allocator<boost::sub_match<std::__1::__wrap_iter<char
const*> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> >
>::match_alt() in SLNParse.cpp.o
boost::re_detail_106000::perl_matcher<std::__1::__wrap_iter<char
const*>, std::__1::allocator<boost::sub_match<std::__1::__wrap_iter<char
const*> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> >
>::match_rep() in SLNParse.cpp.o
boost::re_detail_106000::perl_matcher<std::__1::__wrap_iter<char
const*>, std::__1::allocator<boost::sub_match<std::__1::__wrap_iter<char
const*> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> >
>::match_char_repeat() in SLNParse.cpp.o
...
"boost::re_detail_106000::put_mem_block(void*)", referenced from:
boost::re_detail_106000::perl_matcher<std::__1::__wrap_iter<char
const*>, std::__1::allocator<boost::sub_match<std::__1::__wrap_iter<char
const*> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> >
>::find_imp() in SLNParse.cpp.o
boost::re_detail_106000::perl_matcher<std::__1::__wrap_iter<char
const*>, std::__1::allocator<boost::sub_match<std::__1::__wrap_iter<char
const*> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> >
>::unwind_extra_block(bool) in SLNParse.cpp.o
"boost::re_detail_106000::verify_options(unsigned int,
boost::regex_constants::_match_flags)", referenced from:
boost::re_detail_106000::perl_matcher<std::__1::__wrap_iter<char
const*>, std::__1::allocator<boost::sub_match<std::__1::__wrap_iter<char
const*> > >, boost::regex_traits<char, boost::cpp_regex_traits<char> >
>::find_imp() in SLNParse.cpp.o
"boost::re_detail_106000::raise_runtime_error(std::runtime_error
const&)", referenced from:
void
boost::re_detail_106000::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 SLNParse.cpp.o
"boost::re_detail_106000::get_default_error_string(boost::regex_constants::error_type)",
referenced from:
boost::re_detail_106000::cpp_regex_traits_implementation<char>::error_string(boost::regex_constants::error_type)
const in SLNParse.cpp.o
"boost::re_detail_106000::cpp_regex_traits_implementation<char>::transform_primary(char
const*, char const*) const", referenced from:
std::__1::__wrap_iter<char const*>
boost::re_detail_106000::re_is_set_member<std::__1::__wrap_iter<char
const*>, char, boost::regex_traits<char, boost::cpp_regex_traits<char>
>, unsigned int>(std::__1::__wrap_iter<char const*>,
std::__1::__wrap_iter<char const*>,
boost::re_detail_106000::re_set_long<unsigned int> const*,
boost::re_detail_106000::regex_data<char, boost::regex_traits<char,
boost::cpp_regex_traits<char> > > const&, bool) in SLNParse.cpp.o
"boost::re_detail_106000::cpp_regex_traits_implementation<char>::transform(char
const*, char const*) const", referenced from:
std::__1::__wrap_iter<char const*>
boost::re_detail_106000::re_is_set_member<std::__1::__wrap_iter<char
const*>, char, boost::regex_traits<char, boost::cpp_regex_traits<char>
>, unsigned int>(std::__1::__wrap_iter<char const*>,
std::__1::__wrap_iter<char const*>,
boost::re_detail_106000::re_set_long<unsigned int> const*,
boost::re_detail_106000::regex_data<char, boost::regex_traits<char,
boost::cpp_regex_traits<char> > > const&, bool) in SLNParse.cpp.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see
invocation)
make[2]: *** [lib/libSLNParse.2016.03.1.dev1.dylib] Error 1
make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2
make: *** [all] Error 2
------------------------------------------------------------------------------
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