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. I'd highly suggest using SVN trunk.
That fails to work, in a much worse way than before.
After working with Noel to update the build instructions for
working out of SVN, and upgrading my copy of SWIG to 1.3.40
I got everything built and installed. It doesn't work though.
Here's my test case.
[xavier:~/ftps/openchord] dalke% cat strange.py
import openbabel
obc = openbabel.OBConversion()
obc.SetInFormat("smi")
mol = openbabel.OBMol()
obc.ReadString(mol, "c1ccccc1O")
print "Done."
It crashes in ReadString, which I did by hand.
[xavier:~/ftps/openchord] dalke% python strange.py
Segmentation fault
[xavier:~/ftps/openchord] dalke% gdb `which python`
GNU gdb 6.3.50-20050815 (Apple version gdb-1346) (Fri Sep 18 20:40:51 UTC 2009)
... lines omitted ...
(gdb) run strange.py
Starting program: /usr/bin/python strange.py
Reading symbols for shared libraries .++..... done
Program received signal SIGTRAP, Trace/breakpoint trap.
0x00007fff5fc01028 in __dyld__dyld_start ()
(gdb) cont
Continuing.
Reading symbols for shared libraries . done
Reading symbols for shared libraries .. done
Reading symbols for shared libraries ... done
Reading symbols for shared libraries . done
... many lines omitted ...
Reading symbols for shared libraries . done
Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000090
OpenBabel::SMIBaseFormat::ReadMolecule (this=<value temporarily unavailable,
due to optimizations>, pOb=<value temporarily unavailable, due to
optimizations>, pConv=0x1002791a0) at
/Users/dalke/cvses/ob-trunk/src/formats/smilesformat.cpp:282
282 pmol->SetDimension(0);
To show some context
(gdb) l
277 obErrorLog.ThrowError(__FUNCTION__,
278 smiles + " contained a character '" + smiles[pos] + "' which is
invalid in SMILES", obError);
279 return false;
280 }
281
282 pmol->SetDimension(0);
283 OBSmilesParser sp;
284
285 pos = smiles.find('>');
286 if(pos==string::npos)
and it's a straight NULL pointer deference.
(gdb) print pmol
$1 = (class OpenBabel::OBMol *) 0x0
The call stack.
(gdb) where
#0 OpenBabel::SMIBaseFormat::ReadMolecule (this=<value temporarily
unavailable, due to optimizations>, pOb=<value temporarily unavailable, due to
optimizations>, pConv=0x1002791a0) at
/Users/dalke/cvses/ob-trunk/src/formats/smilesformat.cpp:282
#1 0x000000010146b8bc in OpenBabel::OBConversion::Read (this=0x1002791a0,
pOb=0x100293b70, pin=<value temporarily unavailable, due to optimizations>) at
/Users/dalke/cvses/ob-trunk/src/obconversion.cpp:747
#2 0x000000010147083c in OpenBabel::OBConversion::ReadString
(this=0x1002791a0, pOb=0x100293b70, input=<value temporarily unavailable, due
to optimizations>) at /Users/dalke/cvses/ob-trunk/src/obconversion.cpp:895
#3 0x0000000101155444 in _wrap_OBConversion_ReadString (args=<value
temporarily unavailable, due to optimizations>) at openbabel-python.cpp:17379
#4 0x000000010000aff3 in PyObject_Call ()
#5 0x000000010008a51a in PyEval_EvalFrameEx ()
#6 0x000000010008acce in PyEval_EvalCodeEx ()
#7 0x000000010008ad61 in PyEval_EvalCode ()
#8 0x00000001000a265a in Py_CompileString ()
#9 0x00000001000a2723 in PyRun_FileExFlags ()
#10 0x00000001000a423d in PyRun_SimpleFileExFlags ()
#11 0x00000001000b0286 in Py_Main ()
#12 0x0000000100000e6c in ?? ()
BTW, is there a way to get the version number from OpenBabel?
In trying to get this all working I ran into snags where I was
installed into the wrong directory, and I couldn't figure out
a way to tell if the "import openbabel" I just installed was
the right one, except by looking at the file timestamp.
Ideally I would like to have a way to get the pybel.py,
openbabel.py, and underlying shared library versions.
To make sure I have the right extension modules (I
wondered if I had a version mismatch), I include part
of what Apple's crash reporter says:
0x101816000 - 0x101a3ffff +libopenbabel.4.dylib 4.0.0
(compatibility 4.0.0) <A1B64057-4A8A-520C-AD96-4227D6B58DF5>
/usr/local/lib/libopenbabel.4.dylib
0x1021ca000 - 0x1021e6ff7 +smilesformat.so ??? (???)
<7D01F338-7571-62B5-A8EE-53A1C2C62773>
/usr/local/lib/openbabel/2.2.99/smilesformat.so
and some file stamps
-rwxr-xr-x 1 root wheel 3281376 Apr 12 20:19
/usr/local/lib/libopenbabel.4.0.0.dylib
lrwxr-xr-x 1 root wheel 24 Apr 12 15:22
/usr/local/lib/libopenbabel.4.dylib -> libopenbabel.4.0.0.dylib
-rwxr-xr-x 1 root wheel 211456 Apr 12 20:19
/usr/local/lib/openbabel/2.2.99/smilesformat.so
You can see I do have the right shared library here.
Andrew
da...@dalkescientific.com
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