Hi Greg Thanks for the quick fix. It worked fine, but I ran into another problem that seems worse. It was reported at https://bugzilla.redhat.com/show_bug.cgi?id=444029 and the conclusion was don't use FC8 - it's too old Unless you have some insight into how to remedy this, I'm going to conclude one cannot run rdkit on FC8.
-TJ Here is the relevant output from make: [ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o /usr/local/boost_1_43_0/include/boost/type_traits/detail/cv_traits_impl.hpp: In instantiation of const bool boost::detail::cv_traits_imp<RDKit::<unnamed>::EditableMol*>::is_const: /usr/local/boost_1_43_0/include/boost/type_traits/is_const.hpp:57: instantiated from boost::is_const<RDKit::<unnamed>::EditableMol> /usr/local/boost_1_43_0/include/boost/python/detail/cv_category.hpp:31: instantiated from boost::python::detail::cv_category<RDKit::<unnamed>::EditableMol> /usr/local/boost_1_43_0/include/boost/python/detail/unwind_type.hpp:58: instantiated from typename Generator::result_type boost::python::detail::unwind_ptr_type(U*, Generator*) [with Generator = boost::python::converter::detail::unwind_type_id_helper, U = RDKit::<unnamed>::EditableMol] /usr/local/boost_1_43_0/include/boost/python/detail/unwind_type.hpp:127: instantiated from static typename Generator::result_type boost::python::detail::unwind_helper2<2>::execute(U& (*)(), Generator*) [with Generator = boost::python::converter::detail::unwind_type_id_helper, U = RDKit::<unnamed>::EditableMol] /usr/local/boost_1_43_0/include/boost/python/detail/unwind_type.hpp:165: instantiated from typename Generator::result_type boost::python::detail::unwind_type(boost::type<U>*, Generator*) [with Generator = boost::python::converter::detail::unwind_type_id_helper, U = RDKit::<unnamed>::EditableMol&] /usr/local/boost_1_43_0/include/boost/python/converter/pytype_function.hpp:45: instantiated from boost::python::type_info boost::python::converter::detail::unwind_type_id_(boost::type<Target>*, mpl_::false_*) [with T = RDKit::<unnamed>::EditableMol&] /usr/local/boost_1_43_0/include/boost/python/converter/pytype_function.hpp:68: instantiated from static const PyTypeObject* boost::python::converter::expected_pytype_for_arg<T>::get_pytype() [with T = RDKit::<unnamed>::EditableMol&] /usr/local/boost_1_43_0/include/boost/python/detail/signature.hpp:98: instantiated from static const boost::python::detail::signature_element* boost::python::detail::signature_arity<3u>::impl<Sig>::elements() [with Sig = boost::mpl::vector4<void, RDKit::<unnamed>::EditableMol&, unsigned int, unsigned int>] /usr/local/boost_1_43_0/include/boost/python/detail/caller.hpp:232: instantiated from static boost::python::detail::py_func_sig_info boost::python::detail::caller_arity<3u>::impl<F, Policies, Sig>::signature() [with F = void (RDKit::<unnamed>::EditableMol::*)(unsigned int, unsigned int), Policies = boost::python::default_call_policies, Sig = boost::mpl::vector4<void, RDKit::<unnamed>::EditableMol&, unsigned int, unsigned int>] /usr/local/boost_1_43_0/include/boost/python/object/py_function.hpp:48: instantiated from boost::python::detail::py_func_sig_info boost::python::objects::caller_py_function_impl<Caller>::signature() const [with Caller = boost::python::detail::caller<void (RDKit::<unnamed>::EditableMol::*)(unsigned int, unsigned int), boost::python::default_call_policies, boost::mpl::vector4<void, RDKit::<unnamed>::EditableMol&, unsigned int, unsigned int> >] /home/tj/RDKit/trunk/Code/GraphMol/Wrap/EditableMol.cpp:114: instantiated from here /usr/local/boost_1_43_0/include/boost/type_traits/detail/cv_traits_impl.hpp:37: internal compiler error: in make_rtl_for_nonlocal_decl, at cp/decl.c:5067 Please submit a full bug report, with preprocessed source if appropriate. See <URL:http://bugzilla.redhat.com/bugzilla> for instructions. Preprocessed source stored into /tmp/cc6vEfDG.out file, please attach this to your bugreport. make[2]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o] Error 1 make[1]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all] Error 2 make: *** [all] Error 2 > Hi TJ, > > On Fri, Jul 9, 2010 at 3:11 AM, TJ O'Donnell <t...@acm.org> wrote: >> >> I'm trying to build rdkit on a 64-bit redhat system. >> >> g++ (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46) >> >> I built boost 1.43, the latest flex, and got up to this point >> building rdkit >> >> [ 82%] Building CXX object >> Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o >> Linking CXX shared library libSLNParse.so >> /usr/bin/ld: >> /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libboost_regex.a(cpp_regex_traits.o): >> relocation R_X86_64_32S against `std::basic_string<char, >> std::char_traits<char>, std::allocator<char> >> >::_Rep::_S_empty_rep_storage' can not be used when making a shared >> object; recompile with -fPIC >> /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libboost_regex.a: >> could not read symbols: Bad value >> collect2: ld returned 1 exit status >> make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1 >> make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error >> 2 >> make: *** [all] Error 2 >> >> Can you help? > > looks like you aren't linking against the boost that you built; > instead the system boost is being used. > you could verify this empirically with: > % VERBOSE=1 make SLNParse > > You can try to fix the problem by running: > % ccmake . > (note the extra c) in your build directory, typing "t" to toggle > advanced mode, and manually editing the value for > Boost_REGEX_LIBRARY_RELEASE > > In the meantime, since this is a problem that repeatedly occurs, I'm > going to modify the CMake files to stop using the statically linked > version of libregex.. This will be in svn in the next hour. > > -greg > ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
