[Bioperl-l] DB_File dependency and ActiveState 5.10
Chris Fields
cjfields at illinois.edu
Thu Sep 24 17:50:34 UTC 2009
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
>
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