There's a memory leak in readstring, at least when used with SMILES
string, even with trunk. There is a filed bug -
http://sourceforge.net/tracker/?func=detail&aid=2978796&group_id=40728&atid=428740.
- Noel
On 12 April 2010 08:33, Andrew Dalke <da...@dalkescientific.com> wrote:
> 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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