Hi, It's not clear from your email whether it is a problem with a particular SMILES (i.e. a bug) or all SMILES (i.e. install problem). Can you clarify?
Regarding manual copying of Python packages, you should add the install directory to your PYTHONPATH instead (and maybe complain to MacPorts that they should do this). We install to the location that MacPorts has configured distutils to use (which is typically different than where MacPorts would install it's own Python packages). - Noel On 30 August 2010 18:04, Rajarshi Guha <rajarshi.g...@gmail.com> wrote: > 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 > ------------------------------------------------------------------------------ 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
