[Bioperl-l] Bio::DB::GFF table creation problems/test failures

[Lincoln Stein]

Oh gee, what can I do? I will have to hard-code testing for the particular
version of mysql in order to fix this.

Lincoln

On Mon, Apr 11, 2011 at 2:37 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Lincoln,
>
> Last week you fixed a problem with the way Bio::DB::GFF created MySQL
> tables, removing the "type=MYISAM" from the declaration.  The problem
> now is that when I try to create a new Bio::DB::GFF database, I get
> this error:
>
>  The used table type doesn't support FULLTEXT indexes
>
> when trying to create the fattribute_to_feature table.  It looks like
> the default engine is InnoDB, which doesn't support full text
> searching.  Of course, if I add "ENGINE MYISAM" to the end of the
> query it works.  This is with mysql 5.5.9.  When the table creation
> fails, obviously most of the tests fail when testing against MySQL.
>
> Scott
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>