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#91 Gap4 crashes when opening chromatograms

open
nobody
None
5
2011-06-03
2011-06-03
Warren Gallin
No

I am running Mac OSX 10.6.7, using the executable for v. 1.7.0 downloaded from SourceForge.

When I double click on a consensus character while editting a contig, instead of opening the relevant chromatogram I get a crash. The terminal output is as follows:

null-c82a141309fc:~ wgallin$ gap4
stash(3816) malloc: *** mmap(size=1114701824) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Not enough memory.
Level 1: trace_add .cedit0.0.seqs.traces 12-2622_013.ztr .cedit0.0.seqs { -5 12-2622_013 }
Fri 03 Jun 15:02:42 2011 signal_handler: Program terminated unexpectedly with signal 10.
Fri 03 Jun 15:02:42 2011 signal_handler: This is probably a bug.
Fri 03 Jun 15:02:42 2011 signal_handler: Please report all bug reports at https://sourceforge.net/projects/staden/
Abort trap
null-c82a141309fc:~ wgallin$

Discussion

  • James Bonfield
    James Bonfield
    2011-06-06

    Is this any trace? It looks like it's trying to allocate over 1Gb of memory which is somewhat peculiar.

    However I did just fix a different issue with the trace display which may be related. It too was causing periodic crashes, so please try compiling the latest source out from subversion. Specifically it's revision 2413 to file src/gap4/tman_interface.c:

    http://staden.svn.sourceforge.net/viewvc/staden?view=revision&sortby=date&revision=2413

    I don't see how this would manifest itself as the memory allocation issue you see, but it's worth trying to see if this is the same issue. Perhaps it's simply allocating more stack space.