[Bioperl-l] question about revision 1.17 of Bio::Index::AbstractSeq.pm
smarkel at scitegic.com
Thu Mar 23 20:08:55 EST 2006
Thanks for the detailed response. We're using a version we
compiled, not ActivePerl.
> perl.exe -v
This is perl, v5.8.7 built for MSWin32-x86-multi-thread
We'll go check the DB_File versions again. Hopefully we'll
see something obvious.
Chris Fields wrote:
> 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?
> 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
>> San Diego, CA 92123 fax: +1 858 279 8804
>> USA web: http://www.scitegic.com
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
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
San Diego, CA 92123 fax: +1 858 279 8804
USA web: http://www.scitegic.com
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