Re: For those who would like to debug some old C++ code over the weekend
On 02/14/2014 03:53 PM, Olivier Sallou wrote:
> On 02/14/2014 02:51 PM, Andreas Tille wrote:
>> Hi,
>>
>> I'm currently working on preconditions for ngopt[1] which is used in our
>> institute. It includes some third party pieces of code and one of this
>> is FISH[2]. I have created some packaging for this at
>>
>> svn://anonscm.debian.org/debian-med/trunk/packages/unc-fish/trunk/
>>
>> but when I try to process the provided test data it segfaults:
>>
>> $ /usr/lib/unc-fish/fish -b blocks.txt -B simpleblocks.txt -g grids.txt -C contigs.txt
>> Segmentation fault
> It fails at:
> Program terminated with signal 11, Segmentation fault.
> #0 0xf74fcad6 in vfprintf () from /lib/i386-linux-gnu/libc.so.6
> (gdb) where
> #0 0xf74fcad6 in vfprintf () from /lib/i386-linux-gnu/libc.so.6
> #1 0xf7506ebf in fprintf () from /lib/i386-linux-gnu/libc.so.6
> #2 0x0805166d in grids () at grids.h:278
> #3 0x080540aa in main (argc=11, argv=0xffbd9654) at fish.cpp:341
>
> on fprintf(print_grid, "%s",get_time_stamp());
>
> maybe an issue because get_time_stamp returns a char* or in time-stamp
> settings.
If we comment the fprintf (it is only print issue after all), other
errors are raised on stl_maps in readfile.h ligne 438:
INV_GENE=GENE;
so it seems there are issues with this code.....
Olivier
>
> Olivier
>
>
>> There are some suspicious format warnings when building but the problem
>> might be also somewhere else. Since ngopt is my final target I dived
>> into their repository and have takoen the content of
>>
>> http://code.google.com/p/ngopt/source/browse/#svn%2Ftrunk%2FFISH%2Fsrc
>>
>> as a quilt patch - which at least solves the segfault issue. So without
>> this patch the original code segfaults with the sample data set but due
>> to some other changes the result set of the test code can not be
>> reproduced. (BTW, I found a binary of fish on some non-Debian host used
>> in my institute which runs as well and produces a third result which is
>> different from the original test result and the patched version.)
>>
>> This issue makes me quite suspicious and I wonder whether we could at
>> least reproduce the original test suite with the original code without
>> the segfault problem. Any volunteer to check the code for this issue?
>>
>> Kind regards
>>
>> Andreas.
>>
>> [1] http://code.google.com/p/ngopt/
>> [2] http://labs.bio.unc.edu/Vision/FISH/
>>
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
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