Your message dated Mon, 13 Jan 2025 11:41:13 +0000
with message-id <e1txioj-00dcd9...@fasolo.debian.org>
and subject line Bug#1083076: fixed in rdkit 202409.2-3
has caused the Debian Bug report #1083076,
regarding python3-rdkit: SEGFAULT on import on armhf and armel
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1083076: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1083076
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Source: rdkit
Source-Version: 202409.2-3
Done: Andrius Merkys <mer...@debian.org>
We believe that the bug you reported is fixed in the latest version of
rdkit, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1083...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <mer...@debian.org> (supplier of updated rdkit package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 13 Jan 2025 03:40:17 -0500
Source: rdkit
Architecture: source
Version: 202409.2-3
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Andrius Merkys <mer...@debian.org>
Closes: 1083076
Changes:
rdkit (202409.2-3) unstable; urgency=medium
.
[ Michael Banck ]
* debian/patches/disable_python_test.patch: New patch, disables a python test
that fails on all architectures.
* debian/rules (override_dh_auto_test): No longer ignore testuite failures.
* debian/tests/importcheck: New autopkgtest, tests importing the python
module.
.
[ Andrius Merkys ]
* Drop support for 32bit architectures (Closes: #1083076)
* Cleanup debian/copyright.
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