Hi Again, To update, this is something specific to my desktop as my laptop doesn't seem to have the same problem. Also specific to the github version, when I use 2014.03.1I don't see the same error.
I get an almighty error message, which I have attached. If anyone has any bright ideas, I'd been keen to know. Best, Nick The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Process: Python [66986]
Path:
/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.2 (2.7.2)
Code Type: X86-64 (Native)
Parent Process: bash [35863]
User ID: 17477
PlugIn Path: /usr/local/lib/python2.7/site-packages/rdkit/Chem/rdmolops.so
PlugIn Identifier: rdmolops.so
PlugIn Version: ??? (0)
Date/Time: 2014-10-29 09:17:25.532 +0000
OS Version: Mac OS X 10.8.5 (12F45)
Report Version: 10
Interval Since Last Report: 65511 sec
Crashes Since Last Report: 9
Per-App Crashes Since Last Report: 1
Anonymous UUID: 75E33DCF-56D4-3EF6-A8F3-4B6869D00628
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000010
VM Regions Near 0x10:
-->
__TEXT 0000000100aea000-0000000100aeb000 [ 4K] r-x/rwx
SM=COW
/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 rdmolops.so 0x000000010225845e
RDKit::getDistanceMatrix(RDKit::ROMol&, bool, bool, bool, char const*) + 110
1 rdmolops.so 0x0000000102276def
boost::python::detail::caller_arity<5u>::impl<_object* (*)(RDKit::ROMol&, bool,
bool, bool, char const*), boost::python::default_call_policies,
boost::mpl::vector6<_object*, RDKit::ROMol&, bool, bool, bool, char const*>
>::operator()(_object*, _object*) + 367
2 libboost_python-mt.dylib 0x000000010107537e
boost::python::objects::function::call(_object*, _object*) const + 766
3 libboost_python-mt.dylib 0x000000010107747a
boost::detail::function::void_function_ref_invoker0<boost::python::objects::(anonymous
namespace)::bind_return,
void>::invoke(boost::detail::function::function_buffer&) + 26
4 libboost_python-mt.dylib 0x000000010107d65c
boost::function0<void>::operator()() const + 28
5 libboost_python-mt.dylib 0x000000010107d37c
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 28
6 rdchem.so 0x0000000101c49cfa bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(RDKit::MolSanitizeException const&)> >::operator()<bool,
boost::python::detail::translate_exception<RDKit::MolSanitizeException, void
(*)(RDKit::MolSanitizeException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<RDKit::MolSanitizeException, void
(*)(RDKit::MolSanitizeException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
7 rdchem.so 0x0000000101c49cdd
boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool,
boost::python::detail::translate_exception<RDKit::MolSanitizeException, void
(*)(RDKit::MolSanitizeException const&)>, boost::_bi::list3<boost::arg<1>,
boost::arg<2>, boost::_bi::value<void (*)(RDKit::MolSanitizeException 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&)
+ 35
8 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
9 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
10 rdBase.so 0x0000000100e7291e bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(ValueErrorException const&)> >::operator()<bool,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
11 rdBase.so 0x0000000100e72901
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&)
+ 35
12 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
13 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
14 rdBase.so 0x0000000100e72a02 bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(IndexErrorException const&)> >::operator()<bool,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
15 rdBase.so 0x0000000100e729e5
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&)
+ 35
16 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
17 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
18 rdmolfiles.so 0x0000000102060516 bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(RDKit::BadFileException const&)> >::operator()<bool,
boost::python::detail::translate_exception<RDKit::BadFileException, void
(*)(RDKit::BadFileException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<RDKit::BadFileException, void
(*)(RDKit::BadFileException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
19 rdmolfiles.so 0x00000001020604f9
boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool,
boost::python::detail::translate_exception<RDKit::BadFileException, void
(*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>,
boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException 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&)
+ 35
20 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
21 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
22 rdchem.so 0x0000000101c49cfa bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(RDKit::MolSanitizeException const&)> >::operator()<bool,
boost::python::detail::translate_exception<RDKit::MolSanitizeException, void
(*)(RDKit::MolSanitizeException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<RDKit::MolSanitizeException, void
(*)(RDKit::MolSanitizeException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
23 rdchem.so 0x0000000101c49cdd
boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool,
boost::python::detail::translate_exception<RDKit::MolSanitizeException, void
(*)(RDKit::MolSanitizeException const&)>, boost::_bi::list3<boost::arg<1>,
boost::arg<2>, boost::_bi::value<void (*)(RDKit::MolSanitizeException 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&)
+ 35
24 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
25 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
26 rdBase.so 0x0000000100e7291e bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(ValueErrorException const&)> >::operator()<bool,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
27 rdBase.so 0x0000000100e72901
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&)
+ 35
28 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
29 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
30 rdBase.so 0x0000000100e72a02 bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(IndexErrorException const&)> >::operator()<bool,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
31 rdBase.so 0x0000000100e729e5
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&)
+ 35
32 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
33 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
34 rdchem.so 0x0000000101c8133a bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(RDKit::ConformerException const&)> >::operator()<bool,
boost::python::detail::translate_exception<RDKit::ConformerException, void
(*)(RDKit::ConformerException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<RDKit::ConformerException, void
(*)(RDKit::ConformerException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
35 rdchem.so 0x0000000101c8131d
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&)
+ 35
36 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
37 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
38 rdchem.so 0x0000000101c49cfa bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(RDKit::MolSanitizeException const&)> >::operator()<bool,
boost::python::detail::translate_exception<RDKit::MolSanitizeException, void
(*)(RDKit::MolSanitizeException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<RDKit::MolSanitizeException, void
(*)(RDKit::MolSanitizeException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
39 rdchem.so 0x0000000101c49cdd
boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool,
boost::python::detail::translate_exception<RDKit::MolSanitizeException, void
(*)(RDKit::MolSanitizeException const&)>, boost::_bi::list3<boost::arg<1>,
boost::arg<2>, boost::_bi::value<void (*)(RDKit::MolSanitizeException 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&)
+ 35
40 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
41 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
42 rdBase.so 0x0000000100e7291e bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(ValueErrorException const&)> >::operator()<bool,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
43 rdBase.so 0x0000000100e72901
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&)
+ 35
44 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
45 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
46 rdBase.so 0x0000000100e72a02 bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(IndexErrorException const&)> >::operator()<bool,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
47 rdBase.so 0x0000000100e729e5
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&)
+ 35
48 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
49 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
50 rdBase.so 0x0000000100e7291e bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(ValueErrorException const&)> >::operator()<bool,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
51 rdBase.so 0x0000000100e72901
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&)
+ 35
52 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
53 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
54 rdBase.so 0x0000000100e72a02 bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(IndexErrorException const&)> >::operator()<bool,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
55 rdBase.so 0x0000000100e729e5
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&)
+ 35
56 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
57 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
58 rdBase.so 0x0000000100e7291e bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(ValueErrorException const&)> >::operator()<bool,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
59 rdBase.so 0x0000000100e72901
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&)
+ 35
60 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
61 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
62 rdBase.so 0x0000000100e72a02 bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(IndexErrorException const&)> >::operator()<bool,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
63 rdBase.so 0x0000000100e729e5
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&)
+ 35
64 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
65 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
66 rdBase.so 0x0000000100e7291e bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(ValueErrorException const&)> >::operator()<bool,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
67 rdBase.so 0x0000000100e72901
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&)
+ 35
68 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
69 libboost_python-mt.dylib 0x000000010107d372
boost::python::detail::exception_handler::operator()(boost::function0<void>
const&) const + 18
70 rdBase.so 0x0000000100e72a02 bool
boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void
(*)(IndexErrorException const&)> >::operator()<bool,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&> >(boost::_bi::type<bool>,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>&,
boost::_bi::list2<boost::python::detail::exception_handler const&,
boost::function0<void> const&>&, long) + 22
71 rdBase.so 0x0000000100e729e5
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&)
+ 35
72 libboost_python-mt.dylib 0x000000010107d578
boost::python::detail::exception_handler::handle(boost::function0<void> const&)
const + 40
73 libboost_python-mt.dylib 0x000000010107d1cd
boost::python::handle_exception_impl(boost::function0<void>) + 29
74 libboost_python-mt.dylib 0x0000000101076e83 function_call + 83
75 org.python.python 0x0000000100afe6c6 PyObject_Call + 97
76 org.python.python 0x0000000100b0878d PyEval_EvalFrameEx +
9728
77 org.python.python 0x0000000100b06147 PyEval_EvalCodeEx +
1934
78 org.python.python 0x0000000100b059b3 PyEval_EvalCode + 54
79 org.python.python 0x0000000100b41c70 0x100aef000 + 339056
80 org.python.python 0x0000000100b41ae9
PyRun_InteractiveOneFlags + 518
81 org.python.python 0x0000000100b41578
PyRun_InteractiveLoopFlags + 206
82 org.python.python 0x0000000100b41414 PyRun_AnyFileExFlags
+ 63
83 org.python.python 0x0000000100b65e27 Py_Main + 2715
84 libdyld.dylib 0x00007fff934487e1 start + 1
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000000000002 rcx: 0x0000000000000002
rdx: 0x00007fff5f114250
rdi: 0x00007fa6a90389a0 rsi: 0x0000000000000000 rbp: 0x00007fff5f114290
rsp: 0x00007fff5f114230
r8: 0x00007fa6a9038ab0 r9: 0x000000000000000b r10: 0x0000000000000002
r11: 0x0000000000000800
r12: 0x00000001022a2c08 r13: 0x0000000000000000 r14: 0x00007fa6a903b5c0
r15: 0x00007fa6a906b500
rip: 0x000000010225845e rfl: 0x0000000000010202 cr2: 0x0000000000000010
Logical CPU: 10
Binary Images:
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<EAA2B53E-EADE-39CF-A0EF-FB9D4940672A> /usr/lib/libstdc++.6.dylib
0x7fff92c04000 - 0x7fff92c04fff com.apple.Accelerate (1.8 - Accelerate
1.8) <878A6E7E-CB34-380F-8212-47FBF12C7C96>
/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
0x7fff92ca6000 - 0x7fff92d0efff libvDSP.dylib (380.10)
<3CA154A3-1BE5-3CF4-BE48-F0A719A963BB>
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
0x7fff92e2a000 - 0x7fff93014ff7 com.apple.CoreFoundation (6.8 -
744.19) <0F7403CA-2CB8-3D0A-992B-679701DF27CA>
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x7fff9301e000 - 0x7fff93029fff libsystem_notify.dylib (98.5)
<C49275CC-835A-3207-AFBA-8C01374927B6> /usr/lib/system/libsystem_notify.dylib
0x7fff93446000 - 0x7fff93449ff7 libdyld.dylib (210.2.3)
<F59367C9-C110-382B-A695-9035A6DD387E> /usr/lib/system/libdyld.dylib
0x7fff9344a000 - 0x7fff935d0fff libBLAS.dylib (1073.4)
<C102C0F6-8CB6-3B49-BA6B-2EB61F0B2784>
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
0x7fff936f8000 - 0x7fff93893fef com.apple.vImage (6.0 - 6.0)
<FAE13169-295A-33A5-8E6B-7C2CC1407FA7>
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
0x7fff9457a000 - 0x7fff945c6ff7 libauto.dylib (185.4)
<AD5A4CE7-CB53-313C-9FAE-673303CC2D35> /usr/lib/libauto.dylib
0x7fff94776000 - 0x7fff947c5ff7 libcorecrypto.dylib (106.2)
<CE0C29A3-C420-339B-ADAA-52F4683233CC> /usr/lib/system/libcorecrypto.dylib
0x7fff94c18000 - 0x7fff94c26fff libcommonCrypto.dylib (60027)
<BAAFE0C9-BB86-3CA7-88C0-E3CBA98DA06F> /usr/lib/system/libcommonCrypto.dylib
0x7fff94ffb000 - 0x7fff95031fff libsystem_info.dylib (406.17)
<4FFCA242-7F04-365F-87A6-D4EFB89503C1> /usr/lib/system/libsystem_info.dylib
0x7fff9507c000 - 0x7fff95083fff libcopyfile.dylib (89)
<876573D0-E907-3566-A108-577EAD1B6182> /usr/lib/system/libcopyfile.dylib
0x7fff961a7000 - 0x7fff9620fff7 libc++.1.dylib (65.1)
<20E31B90-19B9-3C2A-A9EB-474E08F9FE05> /usr/lib/libc++.1.dylib
0x7fff96350000 - 0x7fff96351fff libDiagnosticMessagesClient.dylib (8)
<8548E0DC-0D2F-30B6-B045-FE8A038E76D8>
/usr/lib/libDiagnosticMessagesClient.dylib
0x7fff96747000 - 0x7fff96748ff7 libSystem.B.dylib (169.3)
<365477AB-D641-389D-B8F4-A1FAE9657EEE> /usr/lib/libSystem.B.dylib
0x7fff967c9000 - 0x7fff967c9fff com.apple.Accelerate.vecLib (3.8 -
vecLib 3.8) <F565B686-24E2-39F2-ACC3-C5E4084476BE>
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 254734
thread_create: 6
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=87.5M resident=56.3M(64%)
swapped_out_or_unallocated=31.2M(36%)
Writable regions: Total=27.1M written=10.2M(38%) resident=12.7M(47%)
swapped_out=0K(0%) unallocated=14.4M(53%)
REGION TYPE VIRTUAL
=========== =======
MALLOC 17.5M
MALLOC guard page 32K
STACK GUARD 56.0M
Stack 8192K
VM_ALLOCATE 8K
__DATA 3204K
__LINKEDIT 60.7M
__TEXT 26.7M
__UNICODE 544K
shared memory 12K
=========== =======
TOTAL 172.7M
Model: MacPro5,1, BootROM MP51.007F.B03, 12 processors, 6-Core Intel Xeon, 2.66
GHz, 64 GB, SMC 1.39f11
Graphics: ATI Radeon HD 5770, ATI Radeon HD 5770, PCIe, 1024 MB
Memory Module: DIMM 1, 8 GB, DDR3 ECC, 1333 MHz, 0x802C,
0x31384B534631473732505A2D314734443120
Memory Module: DIMM 2, 8 GB, DDR3 ECC, 1333 MHz, 0x802C,
0x31384B534631473732505A2D314734443120
Memory Module: DIMM 3, 8 GB, DDR3 ECC, 1333 MHz, 0x802C,
0x31384B534631473732505A2D314734443120
Memory Module: DIMM 4, 8 GB, DDR3 ECC, 1333 MHz, 0x802C,
0x31384B534631473732505A2D314734443120
Memory Module: DIMM 5, 8 GB, DDR3 ECC, 1333 MHz, 0x802C,
0x31384B534631473732505A2D314734443120
Memory Module: DIMM 6, 8 GB, DDR3 ECC, 1333 MHz, 0x802C,
0x31384B534631473732505A2D314734443120
Memory Module: DIMM 7, 8 GB, DDR3 ECC, 1333 MHz, 0x802C,
0x31384B534631473732505A2D314734443120
Memory Module: DIMM 8, 8 GB, DDR3 ECC, 1333 MHz, 0x802C,
0x31384B534631473732505A2D314734443120
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8E), Broadcom
BCM43xx 1.0 (5.106.98.100.17)
Bluetooth: Version 4.1.7f2 12718, 3 service, 21 devices, 3 incoming serial ports
Network Service: Ethernet 1, Ethernet, en0
Network Service: Ethernet 2, Ethernet, en1
Network Service: Wi-Fi, AirPort, en2
PCI Card: ATI Radeon HD 5770, sppci_displaycontroller, Slot-1
Serial ATA Device: HL-DT-ST DVD-RW GH61N
Serial ATA Device: Hitachi HDS723020BLA642, 2 TB
Serial ATA Device: Hitachi HDS723020BLA642, 2 TB
Serial ATA Device: M4-CT512M4SSD2, 512.11 GB
Serial ATA Device: M4-CT512M4SSD2, 512.11 GB
USB Device: hub_device, apple_vendor_id, 0x9126, 0xfa200000 / 2
USB Device: Keyboard Hub, apple_vendor_id, 0x1006, 0xfa230000 / 6
USB Device: Apple Keyboard, apple_vendor_id, 0x0250, 0xfa232000 / 7
USB Device: Display Audio, apple_vendor_id, 0x1105, 0xfa240000 / 5
USB Device: Display iSight, apple_vendor_id, 0x8508, 0xfa250000 / 4
USB Device: Apple LED Cinema Display, apple_vendor_id, 0x9226, 0xfa260000 / 3
USB Device: BRCM2046 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x5a100000 / 2
USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x8215, 0x5a110000
/ 4
USB Device: USB Receiver, 0x046d (Logitech Inc.), 0xc52b, 0x3a200000 / 2
FireWire Device: built-in_hub, 800mbit_speed
Nicholas C. Firth | PhD Student | Cancer Therapeutics The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey | SM2 5NG T 020 8722 4033 | E [email protected] | W www.icr.ac.uk | Twitter @ICRnews Facebook www.facebook.com/theinstituteofcancerresearch Making the discoveries that defeat cancer |
On 28 Oct 2014, at 15:20, Nicholas Firth <[email protected]> wrote: Hello RDKitters, I'm having a problem with crashing my python every time I call Chem.GetDistanceMatrix. It doesn't seem to matter what molecule I use, it causes Segmentation Fault: 11(everyone's favourite error). I started to dig through the code, but expected to find the function in Code>GraphMol>MolOps but it doesn't appear to be there, although it is in the header file. So I'm a bit stuck. Anyone got any bright ideas? Thanks! Best, Nick Nicholas C. Firth | PhD Student | Cancer Therapeutics The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey | SM2 5NG T 020 8722 4033 | E [email protected] | W www.icr.ac.uk | Twitter @ICRnews Facebook www.facebook.com/theinstituteofcancerresearch Making the discoveries that defeat cancer <image001.gif> |
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