I have a fix for this in the conda recipes I can submit, it boils down to
something like the following ( setting the CXXFLAGS for c++11 )
if otool -L "$PYROOT/lib/libboost_python.dylib" | grep libc++ ; then
FLAGS="-std=c++11 -stdlib=libc++"
else
FLAGS="-stdlib=libstdc++"
fi
CXXFLAGS=$FLAGS \
cmake -DPYTHON_EXECUTABLE=$PYROOT/bin/python \
...
On Tue, Feb 23, 2016 at 10:52 AM, Greg Landrum <[email protected]>
wrote:
>
>
> On Tue, Feb 23, 2016 at 3:50 PM, Paul Emsley <[email protected]>
> wrote:
>
>>
>> This seems to be the relevant difference in the cmake output:
>>
>>
> <snip>
>
>
>>
>> [ 3%] Linking CXX shared library ../../lib/libRDBoost.dylib
>> Undefined symbols for architecture x86_64:
>> "boost::python::throw_error_already_set()", referenced from:
>> throw_index_error(int) in Wrap.cpp.o
>> throw_value_error(std::__1::basic_string<char,
>> std::__1::char_traits<char>, std::__1::allocator<char> >) in Wrap.cpp.o
>> translate_index_error(IndexErrorException const&) in Wrap.cpp.o
>> translate_value_error(ValueErrorException const&) in Wrap.cpp.o
>> throw_runtime_error(std::__1::basic_string<char,
>> std::__1::char_traits<char>, std::__1::allocator<char> >) in Wrap.cpp.o
>> translate_invariant_error(Invar::Invariant const&) in Wrap.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/libRDBoost.2016.03.1.dev1.dylib] Error 1
>> make[1]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2
>> make: *** [all] Error 2
>>
>> These functions are in libboost_python.dylib, but I don't know how to
>> tell cmake how to find them there when linking RDBoost.dylib.
>>
>
> Ah, very good. I think I know this one. The problem tends to be due to a
> mixture of libraries that were built against the new C++ libraries (the
> default with newer versions of clang) and those built using the older C++
> mode. You control this with the -stdlib flag to the C++ compiler. The two
> options are "-stdlib=libc++" (this is the newer library and is now the
> default) or "-stdlib=libstdc++" (this is the older one). The way you
> diagnose this is by looking at the output of otool -L.
>
> Here's a library built using the new one (the default now with homebrew):
>
> ~/rdk/RDKit_git/build_java % otool -L /usr/local/lib/libboost_regex.dylib
> /usr/local/lib/libboost_regex.dylib:
> /usr/local/opt/boost/lib/libboost_regex.dylib (compatibility version
> 0.0.0, current version 0.0.0)
> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version
> 120.1.0)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 1226.10.1)
>
> And here's one built using the older version:
>
> ~/rdk/RDKit_git/build_java % otool -L
> /usr/local/opt/boost_1_48/lib/libboost_regex.dylib
> /usr/local/opt/boost_1_48/lib/libboost_regex.dylib:
> libboost_regex.dylib (compatibility version 0.0.0, current version 0.0.0)
> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version
> 104.1.0)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 1226.10.1)
>
>
> You cannot mix these, but you can control which gets used by cmake as
> follows:
> CXX="/usr/bin/c++ -stdlib=libstdc++" cmake <insert your usual cmake
> arguments here> ..
> or:
> CXX="/usr/bin/c++ -stdlib=libc++" cmake <insert your usual cmake arguments
> here> ..
>
>
>> p.s. Sorry for the delay, now back from my travels.
>>
>
> No worries, it gave me a chance to figure out how to at least diagnose
> these problems.
>
>
>> p.p.s. Is this a list where top-posting is preferred? (I'm an in-line
>> quoter by preference)
>>
>
> I personally prefer in-line, but sometimes will use top-posting if I'm
> lazy or if I'm using gmail on a mobile device (where the in-line quoting
> doesn't always work as well as one might hope).
>
> -greg
>
>
>
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