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 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
