[Debichem-devel] Bug#716567: [Mayhem] Bug report on openbabel: obprobe crashes with exit status 139

[Daniel Leidert]

Package: openbabel
Followup-For: Bug #716567

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Backtrace attached.


- -- 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

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Starting program: /usr/bin/obprobe "`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.
0x00007ffff7a6d764 in __GI_____strtod_l_internal (nptr=0x0, endptr=0x0, group=<optimized out>, loc=0x7ffff7dd5f40 <_nl_global_locale>)
    at strtod_l.c:607
607	strtod_l.c: No such file or directory.
#0  0x00007ffff7a6d764 in __GI_____strtod_l_internal (nptr=0x0, endptr=0x0, group=<optimized out>, loc=0x7ffff7dd5f40 <_nl_global_locale>)
    at strtod_l.c:607
        negative = 0
        num = {0 <repeats 27 times>, 140737351925148, 0, 1, 140737488315472, 11, 226653476, 140737351925148, 0, 1, 140737488315520, 11, 
          2090266759, 140737351927184, 0, 140737348054279, 32660418, 140737348054296, 140737348054244, 0, 127579, 140737348054296, 
          140737354110144, 140737348107216, 140737348107504, 140737336145168, 0, 140737353954024, 140737354110144, 140737336240309, 
          140737348107504, 140737336144160, 4294967296}
        numsize = <optimized out>
        exponent = 0
        base = 10
        den = {140737353968072, 140737488315720, 140737488315680, 140737353954024, 1, 140737353968928, 140737353968072, 140737351927963, 
          0, 140737353954024, 1, 0, 1, 140737353968072, 0, 140737353968928, 226653476, 0, 0, 140737336388396, 0, 140737353968928, 
          2090266759, 140737354110144, 80, 140737336240309, 4294967295, 0, 140737348107216, 140737354110144, 472446402651, 532575944823, 
          80, 0, 0, 0, 0, 206158430211, 472446402651, 532575944823, 1, 140737351865920, 26, 140737339185240, 0, 140737488351127, 3, 
          140737488351099, 3, 140737351945653, 140733193388033, 0, 2, 140737348107216, 140733193388032, 1, 140737488315920, 0, 
          140737488351130}
        densize = <optimized out>
        retval = {0}
        bits = 0
        cp = 0x0
        tp = <optimized out>
        startp = <optimized out>
        start_of_digits = <optimized out>
        expp = <optimized out>
        dig_no = <optimized out>
        int_no = <optimized out>
        lead_zero = <optimized out>
        c = <optimized out>
        decimal = 0x7ffff7b98871 <dot.2485> "."
        decimal_len = 1
        thousands = 0x0
        grouping = 0x0
        cnt = <optimized out>
        current = <optimized out>
        __PRETTY_FUNCTION__ = "____strtod_l_internal"
        lowc = <optimized out>
#1  0x0000000000402649 in atof (__nptr=<optimized out>) at /usr/include/x86_64-linux-gnu/bits/stdlib-float.h:28
No locals.
#2  main (argc=4, argv=0x7fffffffedc8) at /tmp/buildd/openbabel-2.3.2+dfsg/tools/obprobe.cpp:90
        ifile = <optimized out>
        extPos = <optimized out>
        step = 0
        padding = <optimized out>
        basename = {static npos = <optimized out>, 
          _M_dataplus = {<std::allocator<char>> = {<__gnu_cxx::new_allocator<char>> = {<No data fields>}, <No data fields>}, 
            _M_p = 0x6045b8 <std::string::_Rep::_S_empty_rep_storage+24> ""}}
        conv = <incomplete type>
        format_in = <optimized out>
        buffer = '\000' <repeats 22848 times>...
        option = {static npos = <optimized out>, 
          _M_dataplus = {<std::allocator<char>> = {<__gnu_cxx::new_allocator<char>> = {<No data fields>}, <No data fields>}, 
            _M_p = 0x620f38 "\001"}}
        ifs = <incomplete type>
        mol = <incomplete type>
        program_name = 0x7fffffffef7b "/usr/bin/obprobe"
        type = 0x7fffffffef9a "\001"
        format_out = <optimized out>
        filename = {static npos = <optimized out>, 
          _M_dataplus = {<std::allocator<char>> = {<__gnu_cxx::new_allocator<char>> = {<No data fields>}, <No data fields>}, 
            _M_p = 0x6045b8 <std::string::_Rep::_S_empty_rep_storage+24> ""}}
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