[Bioperl-l] DB_File dependency and ActiveState 5.10

[Chris Fields]

I do support doing this for sheer flexibility, but it's not an  
absolute showstopper for ActivePerl.  There is a working DB_File PPM  
available for ActivePerl 5.10.1 in the Trouchelle PPM repo:

http://trouchelle.com/ppm10/

That repo is listed in the 'Suggested' list in the latest PPM4  
Preferences (Repositories tag). I had to install it to fix that WinXP  
Bio::Index bug.

(Based on that Bio::Index modules also have this requirement, at least  
tests were being skipped based on lack of DB_File)

chris

On Sep 24, 2009, at 9:17 AM, Mark A. Jensen wrote:

> Gurus of a db stripe:
>
> ActiveState 5.10 has such a problem with BDB that it
> disables their ppm build of the DB_File module. I know
> what the *ultimate* solution is...however...
>
> I did a quick grep of 'use DB_File' across the trunk, and
> it seems there are two categories of dependency--
>
> (1) use of BDB is an option among other dbms
>      (e.g., among the  Bio::DB::GFF::Adaptor::)
>
> (2) BDB is the developer's personal choice
>    (e.g., possibly Bio::DB::FileCache)
>
> In Bio::DB::Fasta, AnyDBM_File is used to allow the
> user a choice. Are there fundamental reasons not to
> convert the type (2) dependencies to AnyDBM_File?
> I will try to do this (on a branch) if there are no technical
> objections. General derision, however, will only goad
> me into action-
>
> Thanks,
> MAJ
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l