gdb-stacktrace1

tre-crash.txt (text/plain), 4.09 KB, created by Martin Mokrejš on 2011-03-04 22:16:52 UTC

Probably still not fixed?

http://www.mail-archive.com/[e-mail]/msg00005.html


$ gdb python
GNU gdb (Gentoo 7.2 p1) 7.2
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "i686-pc-linux-gnu".
For bug reporting instructions, please see:
<http://bugs.gentoo.org/>...
Reading symbols from /usr/bin/python...done.
(gdb) run tre-test.py
Starting program: /usr/bin/python tre-test.py
process 6666 is executing new program: /usr/bin/python2.6
[Thread debugging using libthread_db enabled]
tre.Fuzzyness(delcost=1,inscost=1,maxcost=2147483647,subcost=1,maxdel=2147483647,maxerr=3,maxins=2147483647,maxsub=2147483647)
Traceback (most recent call last):
  File "tre-test.py", line 11, in <module>
    m = pt.search(data, fz)
SystemError: error return without exception set

Program received signal SIGSEGV, Segmentation fault.
__libc_free (mem=0x706d695f) at malloc.c:3709
3709    malloc.c: No such file or directory.
        in malloc.c
(gdb) where
#0  __libc_free (mem=0x706d695f) at malloc.c:3709
#1  0xb7d9650d in __regfree (preg=0xb7c70448) at regcomp.c:646
#2  0xb7fde4e3 in PyTrePattern_dealloc (self=0xb7c70440) at tre-python.c:409
#3  0xb7ec1287 in insertdict (mp=0xb7cb424c, key=0xb7c772e0, hash=690156838, value=0xb7f87340) at Objects/dictobject.c:459
#4  0xb7ec3b31 in PyDict_SetItem (op=0xb7cb424c, key=0xb7c772e0, value=0xb7f87340) at Objects/dictobject.c:701
#5  0xb7ec5521 in _PyModule_Clear (m=0xb7c8211c) at Objects/moduleobject.c:138
#6  0xb7f2ac44 in PyImport_Cleanup () at Python/import.c:441
#7  0xb7f332cb in Py_Finalize () at Python/pythonrun.c:444
#8  0xb7f3f254 in Py_Main (argc=2, argv=0xbfffe514) at Modules/main.c:609
#9  0x080487fe in main (argc=2, argv=0xbfffe514) at ./Modules/python.c:46
(gdb) bt full
#0  __libc_free (mem=0x706d695f) at malloc.c:3709
        ar_ptr = <value optimized out>
        p = 0x706d6957
#1  0xb7d9650d in __regfree (preg=0xb7c70448) at regcomp.c:646
        dfa = <value optimized out>
#2  0xb7fde4e3 in PyTrePattern_dealloc (self=0xb7c70440) at tre-python.c:409
No locals.
#3  0xb7ec1287 in insertdict (mp=0xb7cb424c, key=0xb7c772e0, hash=690156838, value=0xb7f87340) at Objects/dictobject.c:459
        ep = <value optimized out>
#4  0xb7ec3b31 in PyDict_SetItem (op=0xb7cb424c, key=0xb7c772e0, value=0xb7f87340) at Objects/dictobject.c:701
        hash = <value optimized out>
        n_used = 8
#5  0xb7ec5521 in _PyModule_Clear (m=0xb7c8211c) at Objects/moduleobject.c:138
        s = <value optimized out>
        pos = 7
        key = 0xb7c772e0
        value = 0xb7c70440
        d = 0xb7cb424c
#6  0xb7f2ac44 in PyImport_Cleanup () at Python/import.c:441
        pos = <value optimized out>
        ndone = 1
        name = <value optimized out>
        key = <value optimized out>
        value = 0xb7c8211c
        dict = <value optimized out>
        interp = 0x804b008
        modules = 0xb7c979bc
#7  0xb7f332cb in Py_Finalize () at Python/pythonrun.c:444
        interp = 0x804b008
#8  0xb7f3f254 in Py_Main (argc=2, argv=0xbfffe514) at Modules/main.c:609
        c = <value optimized out>
        sts = 1
        command = 0x0
        filename = 0xbfffe774 "tre-test.py"
        module = 0x0
        fp = <value optimized out>
        p = 0x0
        unbuffered = 1
        skipfirstline = 0
        stdin_is_interactive = 1
        help = 1
        version = 1
        saw_unbuffered_flag = 1
        cf = {cf_flags = 0}
        target_script_name = 0x0
#9  0x080487fe in main (argc=2, argv=0xbfffe514) at ./Modules/python.c:46
        process_name = 0x0
(gdb) 


$ cat tre-test.py 
#! /usr/bin/python

import tre

pt = tre.compile("gaaggcacncaggggataggn", tre.EXTENDED)
data='gactGGCAAGCTCGCTTGATCTTGATTTCTAGATGAGTACAGACGTCGAAGACGGCGTCGACATCTCTGGCTTTGGTTCTAGCAGAGTGTCXgaaagtagtacgtggaggcgaaggcacncaggggataggn'
fz = tre.Fuzzyness(maxerr = 3)

print fz

m = pt.search(data, fz)

if m:
    print m.groups()
    print m[0]
$