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::EditableMol*>::is_const:
/usr/local/boost_1_43_0/include/boost/type_traits/is_const.hpp:57:
instantiated from boost::is_const::EditableMol>
/usr/local/boost_1_43_0/include/boost/python/detail/cv_category.hpp:31:
instantiated from
boost::python::detail::cv_category::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 =
RDKitEditableMol]
/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 = RDKitEditableMol]
/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*, Generator*) [with
Generator = boost::python::converter::detail::unwind_type_id_helper, U =
RDKitEditableMol&]
/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*,
mpl_::false_*) [with T = RDKitEditableMol&]
/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::get_pytype() [with T
= RDKitEditableMol&]
/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::elements() [with
Sig = boost::mpl::vector4::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::signature() [with F = void
(RDKitEditableMol::*)(unsigned int, unsigned int), Policies =
boost::python::default_call_policies, Sig = boost::mpl::vector4::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::signature() const
[with Caller = boost::python::detail::caller::EditableMol::*)(unsigned int, unsigned int),
boost::python::default_call_policies, boost::mpl::vector4::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 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 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> std::char_traits, std::allocator
>> >::_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?
>
> lo
