Package: python3-rdkit
Version: 202309.3-7
Severity: important
Hello,
python3-rdkit encounters SEGFAULT on import on armhf:
$ python3
Python 3.12.6 (main, Sep 7 2024, 14:20:15) [GCC 14.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import Chem
Segmentation fault
gdb output:
$ echo from rdkit import Chem > test.py
$ gdb python3
(gdb) run test.py
Starting program: /usr/bin/python3 test.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library
"/lib/arm-linux-gnueabihf/libthread_db.so.1".
Program received signal SIGSEGV, Segmentation fault.
0xf751c198 in boost::python::objects::enum_base::add_value(char const*,
long) () from /lib/arm-linux-gnueabihf/libboost_python312.so.1.83.0
(gdb) bt
#0 0xf751c198 in boost::python::objects::enum_base::add_value(char
const*, long) () from /lib/arm-linux-gnueabihf/libboost_python312.so.1.83.0
#1 0xf572d108 in init_module_rdmolfiles() () from
/usr/lib/python3/dist-packages/rdkit/Chem/rdmolfiles.cpython-312-arm-linux-gnueabihf.so
#2 0xf752549e in
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const () from /lib/arm-linux-gnueabihf/libboost_python312.so.1.83.0
#3 0xf60b354e in
boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool,
boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded,
void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>,
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool,
boost::python::detail::exception_handler const&, boost::function0<void>
const&>::invoke(boost::detail::function::function_buffer&,
boost::python::detail::exception_handler const&, boost::function0<void>
const&) ()
from
/usr/lib/python3/dist-packages/rdkit/Chem/rdCIPLabeler.cpython-312-arm-linux-gnueabihf.so
#4 0xf5e77322 in
boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool,
boost::python::detail::translate_exception<RDKit::ConformerException,
void (*)(RDKit::ConformerException const&)>,
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(RDKit::ConformerException const&)> > >, bool,
boost::python::detail::exception_handler const&, boost::function0<void>
const&>::invoke(boost::detail::function::function_buffer&,
boost::python::detail::exception_handler const&, boost::function0<void>
const&) () from
/usr/lib/python3/dist-packages/rdkit/Chem/rdchem.cpython-312-arm-linux-gnueabihf.so
#5 0xf5e241e2 in ?? () from
/usr/lib/python3/dist-packages/rdkit/Chem/rdchem.cpython-312-arm-linux-gnueabihf.so
#6 0xf5e2419a in ?? () from
/usr/lib/python3/dist-packages/rdkit/Chem/rdchem.cpython-312-arm-linux-gnueabihf.so
#7 0xf5e24152 in ?? () from
/usr/lib/python3/dist-packages/rdkit/Chem/rdchem.cpython-312-arm-linux-gnueabihf.so
#8 0xf5e2410a in ?? () from
/usr/lib/python3/dist-packages/rdkit/Chem/rdchem.cpython-312-arm-linux-gnueabihf.so
#9 0xf5e240c2 in ?? () from
/usr/lib/python3/dist-packages/rdkit/Chem/rdchem.cpython-312-arm-linux-gnueabihf.so
#10 0xf7bb73de in
boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool,
boost::python::detail::translate_exception<Invar::Invariant, void
(*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>,
boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >,
bool, boost::python::detail::exception_handler const&,
boost::function0<void>
const&>::invoke(boost::detail::function::function_buffer&,
boost::python::detail::exception_handler const&, boost::function0<void>
const&) () from
/usr/lib/python3/dist-packages/rdkit/rdBase.cpython-312-arm-linux-gnueabihf.so
#11 0xf7bb7416 in
boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool,
boost::python::detail::translate_exception<KeyErrorException, void
(*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>,
boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> >
>, bool, boost::python::detail::exception_handler const&,
boost::function0<void>
const&>::invoke(boost::detail::function::function_buffer&,
boost::python::detail::exception_handler const&, boost::function0<void>
const&) () from
/usr/lib/python3/dist-packages/rdkit/rdBase.cpython-312-arm-linux-gnueabihf.so
#12 0xf7bb744e in
boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>,
boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> >
>, bool, boost::python::detail::exception_handler const&,
boost::function0<void>
const&>::invoke(boost::detail::function::function_buffer&,
boost::python::detail::exception_handler const&, boost::function0<void>
const&) () from
/usr/lib/python3/dist-packages/rdkit/rdBase.cpython-312-arm-linux-gnueabihf.so
#13 0xf7bb7486 in
boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>,
boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> >
>, bool, boost::python::detail::exception_handler const&,
boost::function0<void>
const&>::invoke(boost::detail::function::function_buffer&,
boost::python::detail::exception_handler const&, boost::function0<void>
const&) () from
/usr/lib/python3/dist-packages/rdkit/rdBase.cpython-312-arm-linux-gnueabihf.so
#14 0xf7525200 in
boost::python::handle_exception_impl(boost::function0<void>) () from
/lib/arm-linux-gnueabihf/libboost_python312.so.1.83.0
#15 0xf7525d2c in ?? () from
/lib/arm-linux-gnueabihf/libboost_python312.so.1.83.0
#16 0xf7525b2e in boost::python::detail::init_module(PyModuleDef&, void
(*)()) () from /lib/arm-linux-gnueabihf/libboost_python312.so.1.83.0
#17 0x001d3c16 in ?? ()
Backtrace stopped: previous frame identical to this frame (corrupt stack?)
I am working on updating rdkit to 202403.6, will check the issue with
newer version.
Andrius
