[Debichem-devel] Bug#1083076: python3-rdkit: SEGFAULT on import on armhf

[Andrius Merkys]

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