Hey Greg,
I already compiled boost using the instructions from the rdkit wiki. Anyway,
recompiling rdkit completely solves this problem.
But that wasn't easy enough. Next error :
[ 84%] Built target rdSLNParse
[ 85%] Building CXX object
Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o
/root/pool/include/boost/type_traits/detail/cv_traits_impl.hpp: In
instantiation of ‘const bool
boost::detail::cv_traits_imp<RDKit::<unnamed>::EditableMol*>::is_const’:
/root/pool/include/boost/type_traits/is_const.hpp:57: instantiated from
‘boost::is_const<RDKit::<unnamed>::EditableMol>’
/root/pool/include/boost/python/detail/cv_category.hpp:31: instantiated from
‘boost::python::detail::cv_category<RDKit::<unnamed>::EditableMol>’
/root/pool/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]’
/root/pool/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]’
/root/pool/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&]’
/root/pool/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&]’
/root/pool/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&]’
/root/pool/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>]’
/root/pool/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>]’
/root/pool/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> >]’
/usr/local/RDKit_Q22010_1/Code/GraphMol/Wrap/EditableMol.cpp:114:
instantiated from here
/root/pool/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/ccgSaXge.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
I saw this error online also, and people suggested to add the
BOOST_PYTHON_NO_PY_SIGNATURES
flag, and recompile boost, which is what I did, but no effect on this error.
Someone has an idea? Are there plans to come around these boost dependencies in
rdkit...it's a real showstopper on older systems...real pain to get it
installed :(
Cheers.
Peter
On 24/07/2010, at 05:39, Greg Landrum wrote:
> On Sat, Jul 24, 2010 at 5:31 AM, Greg Landrum <[email protected]> wrote:
>> On Fri, Jul 23, 2010 at 11:20 PM, Peter Schmidtke <[email protected]> wrote:
>>> Dear Greg,
>>>
>>> thanks for the hint, but this one changes absolutely nothing to the
>>> compilation for me...unfortunately (I completely redid the whole
>>> compilation and ended up with the same error)
>>>
>>> Any ideas of how to debug this?
>>>
>>
>> Did you re-run cmake? That change should have made it so that you
>> don't need the static regex library at all (which is the source of the
>> problems).
>>
>
> One last suggestion before I leave for the weekend. If re-running
> cmake and then rebuilding doesn't work, you might want to try
> re-building boost following the instructions on the wiki
> (http://code.google.com/p/rdkit/wiki/BuildingWithCmake):
> ./bjam address-model=64 cflags=-fPIC cxxflags=-fPIC install
>
> Best,
> -greg
Peter Schmidtke
-----------------
PhD Student
Department of Physical Chemistry
School of Pharmacy
University of Barcelona
Barcelona, Spain
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