#528 babel crash on reading cif file on MacOSX

[Raik Brinkmann]

babel "Open Babel 2.2.1 -- Mar 1 2009 -- 19:20:41" crashes
on "Darwin 9.7.0 Darwin Kernel Version 9.7.0: Tue Mar 31 22:52:17 PDT 2009; root:xnu-1228.12.14~1/RELEASE_I386 i386"
for "babel -i cif 2aev.cif -o pdb test2.pdb"
with
==============================
*** Open Babel Warning in Init
Unable to open data file 'space-groups.txt'
==============================
*** Open Babel Warning in Init
Cannot initialize database
Segmentation fault

at

Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_INVALID_ADDRESS at address: 0xfffffffc
0x937666e1 in __gnu_cxx::__exchange_and_add ()

1 0x93756070 in std::string::_Rep::_M_dispose ()

2 0x937580a6 in std::string::assign ()

3 0x000ddac5 in OpenBabel::CIFData::ExtractSpacegroup ()

4 0x000e07a7 in OpenBabel::CIFData::ExtractAll ()

5 0x000e2c8f in OpenBabel::CIF::CIF ()

6 0x000e2ddc in OpenBabel::CIFFormat::ReadMolecule ()

7 0x0030eaea in OpenBabel::OBMoleculeFormat::ReadChemObjectImpl ()

8 0x0000f4d8 in OpenBabel::OBMoleculeFormat::ReadChemObject ()

9 0x002f80e8 in OpenBabel::OBConversion::Convert ()

10 0x002f9f44 in OpenBabel::OBConversion::Convert ()

11 0x002fa96d in OpenBabel::OBConversion::FullConvert ()

12 0x00002ea0 in main ()

[Raik Brinkmann]

example cif

[Jean Bréfort]

The space-groups.txt is not installed or installed at the wrong place.

[Raik Brinkmann]

Ok, then it seems this is an installation problem:

I use the precompiled install package. I found the following files:

-rw-r--r-- 1 raik wheel 104997 10 Jul 17:40 /usr/local/share/openbabel/2.2.2/space-groups.txt
-rw-r--r-- 1 raik wheel 104997 10 Jul 17:34 /usr/local/share/openbabel/2.2.2b6/space-groups.txt

I use this binary: /usr/local/bin/babel

[Raik Brinkmann]

Additional remark: When I use babel from the Avogadro package it seems to work, however this is a different version (2.2.2b1) and it produces the same warning message nevertheless.

/Applications/Avogadro.app/Contents/bin/babel
Open Babel 2.2.2b1 -- Jun 2 2009 -- 12:15:39

/Applications/Avogadro.app/Contents/bin/babel -i cif 2aev.cif -o pdb test.pdb

*** Open Babel Warning in Init
Unable to open data file 'space-groups.txt'
==============================
*** Open Babel Warning in Init
Cannot initialize database
==============================
*** Open Babel Warning in Find
Unknown space group with incomplete or wrong definition.
1 molecule converted
3 warnings 80 audit log messages 1 debugging messages

[Geoff Hutchison]

I'm closing this -- it was fixed in 2.2.2. The version from Avogadro 0.9.5 is old, and the 2.2.1 version you report for the initial bug report is also vulnerable.

If you use 2.2.2-release or later, you should be fine.

Thanks for the report!