On Apr 12, 2010, at 3:04 AM, Geoffrey Hutchison wrote:
> You don't mention what version of OB you're using, but imply it's not the
> latest development code.
It was listed in the stack trace:
/Users/dalke/ftps/openbabel-2.2.3/include/openbabel/obconversion.h:256
> I'd highly suggest using SVN trunk. It has completely improved
> stereochemistry handling, and I've run it through ZINC and the older NCI
> database and fixed a variety of crashes and exposed during fragment
> generation.
That being the case, what are the plans for a new release? According
to the main OB page:
• 2009-07-31 Open Babel 2.2.3 Released
• 2009-07-10 Open Babel 2.2.2 Released
• 2009-02-03 Open Babel 2.2.1 Released
• 2008-07-04 Open Babel 2.2.0 Released
which suggests it's well time for a new one.
> I'll give this newer NCI database a try tomorrow when I get to my office.
> Obviously, if I turn up memory corruption, I'll fix that.
I hope you do, but TJ was not able to reproduce it under his Linux build.
BTW, I ran the code under the Mac's memory checkers last night.
It just crashed now with no extra helpful information. The stack
trace again points to smilesformat.so
Thread 0 Crashed: Dispatch queue: com.apple.main-thread
0 libstdc++.6.dylib 0x00007fff861e47cd __dynamic_cast + 89
1 smilesformat.so 0x0000000101a21d8e
OpenBabel::SMIBaseFormat::ReadMolecule(OpenBabel::OBBase*,
OpenBabel::OBConversion*) + 78 (base.h:254)
2 libopenbabel.3.dylib 0x00000001013dfe2c
OpenBabel::OBConversion::Read(OpenBabel::OBBase*, std::istream*) + 220
(obconversion.cpp:745)
3 libopenbabel.3.dylib 0x00000001013e3f4c
OpenBabel::OBConversion::ReadString(OpenBabel::OBBase*, std::string) + 508
(obconversion.cpp:893)
4 _openbabel.so 0x0000000101135d6c
_wrap_OBConversion_ReadString + 881
5 org.python.python 0x000000010000aff3 PyObject_Call + 112
6 org.python.python 0x000000010008a51a PyEval_EvalFrameEx +
20328
7 org.python.python 0x000000010008acce PyEval_EvalCodeEx +
1803
8 org.python.python 0x000000010008ad61 PyEval_EvalCode + 54
9 org.python.python 0x00000001000a265a Py_CompileString + 78
10 org.python.python 0x00000001000a2723 PyRun_FileExFlags +
150
11 org.python.python 0x00000001000a423d
PyRun_SimpleFileExFlags + 704
12 org.python.python 0x00000001000b0286 Py_Main + 2718
13 org.python.python.app 0x0000000100000e6c start + 52
but that's just saying that a dynamic cast is failing, and not that the
smilesformat code contains the error:
T* CastAndClear(bool clear=true)
{
T* pOb = dynamic_cast<T*>(this); // base.h:254 is this line
if(pOb && clear)// Clear only if this is of target class
Clear();
return pOb;
}
Andrew
da...@dalkescientific.com
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