[Bioperl-l] question about revision 1.17 of Bio::Index::AbstractSeq.pm
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
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
> 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 Markel, Ph.D.
> Principal Bioinformatics Architect email: smarkel at scitegic.com
> SciTegic Inc. mobile: +1 858 205 3653
> 9665 Chesapeake Drive, Suite 401 voice: +1 858 279 8800, ext. 253
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