[Debichem-devel] Bug#716203: [Mayhem] Bug report on openbabel: obminimize crashes with exit status 139

[Daniel Leidert]

Package: openbabel
Followup-For: Bug #716203

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Attached the backtrace.


- -- System Information:
Debian Release: jessie/sid
  APT prefers unstable
  APT policy: (850, 'unstable'), (700, 'testing'), (560, 'stable'), (500, 'oldstable'), (110, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 3.10-2-amd64 (SMP w/2 CPU cores)
Locale: LANG=de_DE.utf8, LC_CTYPE=de_DE.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash

Versions of packages openbabel depends on:
ii  libc6          2.17-92
ii  libgcc1        1:4.8.1-8
ii  libgomp1       4.8.1-8
ii  libopenbabel4  2.3.2+dfsg-1
ii  libstdc++6     4.8.1-8
ii  zlib1g         1:1.2.8.dfsg-1

openbabel recommends no packages.

openbabel suggests no packages.

- -- no debconf information

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.14 (GNU/Linux)

iEYEARECAAYFAlIG2pMACgkQm0bx+wiPa4z3LgCdGa6EGCI5Zn3XCuOap4JlwKh4
6/oAn2Re6aGc77fyV38+BZhM00oO0H+L
=uE+H
-----END PGP SIGNATURE-----
-------------- next part --------------
Starting program: /usr/bin/obminimize "`cat argv_1.symb`" "`cat argv_2.symb`" "`cat argv_3.symb`" < "file___dev__stdin.symb"
warning: Could not load shared library symbols for linux-vdso.so.1.
Do you need "set solib-search-path" or "set sysroot"?
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".

Program received signal SIGSEGV, Segmentation fault.
__strlen_sse2 () at ../sysdeps/x86_64/multiarch/../strlen.S:31
31	../sysdeps/x86_64/multiarch/../strlen.S: No such file or directory.
#0  __strlen_sse2 () at ../sysdeps/x86_64/multiarch/../strlen.S:31
No locals.
#1  0x00007ffff6f8ad84 in std::string::assign(char const*) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
No symbol table info available.
#2  0x0000000000402361 in operator= (__s=<optimized out>, this=0x7fffffffe600) at /usr/include/c++/4.8/bits/basic_string.h:555
No locals.
#3  main (argc=4, argv=0x7fffffffedc8) at /tmp/buildd/openbabel-2.3.2+dfsg/tools/obminimize.cpp:158
        ifile = <optimized out>
        extPos = <optimized out>
        crit = 9.9999999999999995e-07
        option2 = <optimized out>
        conv = <incomplete type>
        sd = false
        cut = false
        newton = false
        hydrogens = true
        option = {static npos = <optimized out>, 
          _M_dataplus = {<std::allocator<char>> = {<__gnu_cxx::new_allocator<char>> = {<No data fields>}, <No data fields>}, 
            _M_p = 0x6875f8 "-h"}}
        format_out = 0x0
        mol = <incomplete type>
        steps = 2500
        rvdw = 6
        rele = 10
        freq = 10
        filename = {static npos = <optimized out>, 
          _M_dataplus = {<std::allocator<char>> = {<__gnu_cxx::new_allocator<char>> = {<No data fields>}, <No data fields>}, 
            _M_p = 0x604438 <std::string::_Rep::_S_empty_rep_storage+24> ""}}
        ff = {static npos = <optimized out>, 
          _M_dataplus = {<std::allocator<char>> = {<__gnu_cxx::new_allocator<char>> = {<No data fields>}, <No data fields>}, 
            _M_p = 0x620f38 "MMFF94"}}
        ofs = <incomplete type>
        program_name = 0x7fffffffef71 "/usr/bin/obminimize"
        basename = {static npos = <optimized out>, 
          _M_dataplus = {<std::allocator<char>> = {<__gnu_cxx::new_allocator<char>> = {<No data fields>}, <No data fields>}, 
            _M_p = 0x604438 <std::string::_Rep::_S_empty_rep_storage+24> ""}}
        oext = <optimized out>
        format_in = <optimized out>
        ifs = <incomplete type>
        pFF = <optimized out>
A debugging session is active.

	Inferior 1 [process 16936] will be killed.

Quit anyway? (y or n)