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[perl #36903] Regular expression causes segfault

From:
Steve Peters via RT
Date:
March 29, 2006 09:32
Subject:
[perl #36903] Regular expression causes segfault
Message ID:
rt-3.0.11-36903-131655.5.42906765541318@perl.org
> [mith@ceh.ac.uk - Mon Aug 15 06:22:48 2005]:
> 
> 
> This is a bug report for perl from mith@ceh.ac.uk,
> generated with the help of perlbug 1.35 running under perl v5.8.6.
> 
> 
> -----------------------------------------------------------------
> [Please enter your report here]
> 
> An application I've written that uses regular expressions to
> search for repetitive sequences in genomes sometimes segfaults.
> I've reproduced this on Linux and SunOS. The problem does not
> occur when perl 5.9.2 is used (installed separately in /opt/perl).
> A script containing the affected parts of the application is
> here:
> http://www.genomics.ceh.ac.uk/~milo/perl/testcode.pl
> This data causes the segfault:
> http://www.genomics.ceh.ac.uk/~milo/perl/fault_yes.fasta (2.7M)
> This data does not:
> http://www.genomics.ceh.ac.uk/~milo/perl/fault_no.fasta (2.6M)
> The problem may be connected to large numbers of "N" bases in
> the sequence. These should be ignored by the script, but have
> to be included in the sequence.
> 

Due to permissions, the test code cannot be accessed.  Please fix the
permissions so the code can be accessed.

steve@kirk:~/smoke/perl-current$ wget
http://www.genomics.ceh.ac.uk/~milo/perl/testcode.pl
--11:31:23--  http://www.genomics.ceh.ac.uk/~milo/perl/testcode.pl
           => `testcode.pl'
Resolving www.genomics.ceh.ac.uk... 192.171.160.230
Connecting to www.genomics.ceh.ac.uk|192.171.160.230|:80... connected.
HTTP request sent, awaiting response... 403 Forbidden
11:31:24 ERROR 403: Forbidden.





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