[Bioperl-l] question about revision 1.17 of Bio::Index::AbstractSeq.pm

Chris Fields cjfields at uiuc.edu
Wed Mar 22 20:58:02 EST 2006

Does this have anything to do with older versions of ActivePerl on  
Windows?  I remember seeing something once quite a while back on a  
DB_File bug that was win32-related so I did some searching, but I  
believe that has been fixed in more recent ActivePerl distributions.   
Nathan's fix was probably commented out for newer versions of  

The original bug fix looks like it was intended as a workaround for  
an older DB_File issue in early versions of ActivePerl 5.6 (rev.  
1.15, Jason's original fix whic adds this line, reads "workaround for  
problems with Windows and indexing files - important that latest  
DB_File is installed").   That was over four years ago and dates to  
around the time ActivePerl was having some issues with DB_File.   
ActivePerl DB_File should be working fine now.  Is it possible that  
your ActivePerl version is an older v. 5.6 and has an older, possibly  
buggy DB_File?


On Mar 22, 2006, at 4:28 PM, Scott Markel wrote:

> We're upgrading our Pipeline Pilot Sequence Analysis Collection,
> which runs on Windows and Linux, to use BioPerl 1.5.1.  In
> tracking down a regression change, we've discovered the
> following.
> There's a line in Bio::Index::AbstractSeq that was commented
> out in revision 1.17.  It's the only change.  The CVS log
> message for this change is "Nathan's additions".
> The line is in the fetch() subroutine.
> $begin-- if( $^O =~ /mswin/i); # workaround for Win DB_File bug
> We find that we need this line to be uncommented in order for
> the first character of the ID to be included.
> Anyone have any history on why this line was commented out?
> We looked at DB_File and SDBM_File changes and didn't see
> any changes that impact the file pointer.
> Scott
> -- 
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect  email:  smarkel at scitegic.com
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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