Thanks for the pointer, that seemed to work. It's working now (thouhg I still had to manually copy the Python package from /usr/local/openbabel/lib/python2.5/site-packages/ to my system wide location).
But on running a small script that goes through a SMILES file I got a bus error. here's the report: Process: Python [54607] Path: /System/Library/Frameworks/Python.framework/Versions/2.5/Resources/Python.app/Contents/MacOS/Python Identifier: Python Version: ??? (???) Code Type: X86 (Native) Parent Process: bash [38238] Interval Since Last Report: 1452199 sec Crashes Since Last Report: 39 Per-App Interval Since Last Report: 0 sec Per-App Crashes Since Last Report: 1 Date/Time: 2010-08-30 13:00:53.730 -0400 OS Version: Mac OS X 10.5.8 (9L31a) Report Version: 6 Anonymous UUID: A2D98871-6D26-4F54-8678-AD4490B75C0A Exception Type: EXC_BAD_ACCESS (SIGBUS) Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000000 Crashed Thread: 0 Thread 0 Crashed: 0 smilesformat.so 0x02094f66 OpenBabel::SMIBaseFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*) + 1142 (smilesformat.cpp:277) 1 libopenbabel.4.dylib 0x00529269 OpenBabel::OBConversion::Read(OpenBabel::OBBase*, std::basic_istream<char, std::char_traits<char> >*) + 217 (obconversion.cpp:773) 2 libopenbabel.4.dylib 0x005295c3 OpenBabel::OBConversion::ReadFile(OpenBabel::OBBase*, std::basic_string<char, std::char_traits<char>, std::allocator<char> >) + 403 (obconversion.cpp:979) 3 _openbabel.so 0x010d132b _wrap_OBConversion_ReadFile + 859 (openbabel-python.cpp:18106) 4 org.python.python 0x00121505 PyObject_Call + 50 5 org.python.python 0x0018f832 PyEval_EvalFrameEx + 17904 6 org.python.python 0x00132960 _PyExc_Fini + 1438 7 org.python.python 0x0018ee23 PyEval_EvalFrameEx + 15329 8 org.python.python 0x00191173 PyEval_EvalCodeEx + 1638 9 org.python.python 0x00191260 PyEval_EvalCode + 87 10 org.python.python 0x001a883c PyErr_Display + 1896 11 org.python.python 0x001a8e66 PyRun_FileExFlags + 135 12 org.python.python 0x001aa7d2 PyRun_SimpleFileExFlags + 421 13 org.python.python 0x001b5a57 Py_Main + 3095 14 org.python.pythonapp 0x00001fca 0x1000 + 4042 Thread 1: 0 libSystem.B.dylib 0x921da6fa select$DARWIN_EXTSN + 10 1 libSystem.B.dylib 0x921bc155 _pthread_start + 321 2 libSystem.B.dylib 0x921bc012 thread_start + 34 Thread 0 crashed with X86 Thread State (32-bit): eax: 0xbfffe1dc ebx: 0x02094b04 ecx: 0x00328c9c edx: 0x00000000 edi: 0xbfffe1e6 esi: 0x00328c90 ebp: 0xbfffe208 esp: 0xbfff5ff0 ss: 0x0000001f efl: 0x00010282 eip: 0x02094f66 cs: 0x00000017 ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 cr2: 0x00000000 <snip> On Mon, Aug 30, 2010 at 12:49 PM, Geoffrey Hutchison <ge...@geoffhutchison.net> wrote: >> It turns out that I have v4 of the dylibs > > Do you have Open Babel installed anywhere else? You mentioned MacPorts. Did > you install OB at any point using MacPorts? I'd check /opt for a "v3" dylib. > Something is picking that up. > > Hope that helps, > -Geoff -- Rajarshi Guha NIH Chemical Genomics Center ------------------------------------------------------------------------------ This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
