[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  
ActivePerl.

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?

Chris

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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