[Bioperl-l] BerkeleyDB required for t/Registry.t

Brian Osborne osborne1 at optonline.net
Mon Sep 25 13:16:48 EDT 2006


Nathan,

>From the Flat Databases HOWTO:

Currently there are two indexing schemes supported: "bdb" and "flat".

"bdb" selects an index based on the Berkeley DB library. It is generally the
faster of the two, but it requires that the Berkeley DB library (from Linux
RPM or from SleepyCat, version 2 or higher) and the Perl BerkeleyDB module
be installed on your system. The Perl DB_File module will not work!

"flat" is a sorted text-based index that uses a binary search algorithm to
rapidly search for entries. Although not as fast as bdb, the flat indexing
system has good performance for even large databases, and it has no
requirements beyond Perl itself. The disadvantage of "flat" is that the
indexing of large databases will be slower and more memory-intensive than
the indexing using "bdb".

So strictly speaking the BerkeleyDB module is not required, you can do
"flat". However, "require DB_File" is not true, it's not required so this
can be removed.

Brian O.


On 9/25/06 12:27 PM, "Nathan Haigh" <n.haigh at sheffield.ac.uk> wrote:

> In t/Registry.t there is both a "require DB_File" and "require
> BerkeleyDB", however, there is no mention of BerkeleyDB as being a
> prerequisite of any type in Makefile.PL, has this just slipped through
> the next or is there another reason?
> 
> Some of these tests failed because I didn't have BerkeleyDB installed -
> I did have DB_File though.
> 
> Cheers
> Nath
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