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

Scott Markel smarkel at scitegic.com
Thu Mar 23 20:08:55 EST 2006


Chris,

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.

Scott

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?
> 
> 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
>> 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
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 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



More information about the Bioperl-l mailing list