[Biopython-dev] Re: Work towards getting KDTree compiling

[Marc Colosimo]

On May 10, 2004, at 4:17 PM, Brad Chapman wrote:

> Hi Michiel;
>
> [mingw32]
>
[snip]
>
> [Sun]
>
[snip]
>
> [Mac OS X]
>>> Hmmm. How do they crash? Just a core dump? Can you attach gdb and
>>> see anything? Also, is this with gcc? What versions? For the record,
>>> I'm compiling with gcc version 2.95.4 and 3.3.3 without any
>>> problems.
>>>
>>
>> I'm not sure if this will help much but this is what I get from gdb:
>>
>>>>> from Bio.KDTree import *
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries 
>> bfd_mach_o_scan_read_symtab_symbol:
>> symbol name out of range (399792 >= 5512)
>> . done
>>
>> Program received signal EXC_BAD_ACCESS, Could not access memory.
>> 0x8fe0cc18 in __dyld_is_symbol_coalesced ()
>> (gdb)
>
> Bleah. Some kind of memory leak when loading the libraries -- I have
> zero idea what that means or how to fix it. If it compiles decently,
> then I'll leave it right now, and just hope that some Mac OS people
> can come up with a reason/solution for this. Anyone else with OS X
> can confirm?
>
> Otherwise, well -- I have no idea what to do.
>

With both the Mac and  fink version of python, it works fine for me 
(two different systems, both 10.3.3). Did you install some  other odd 
python package or gcc?