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

[Scott Cain]

I know.  I guess the question is, how far back is the "ENGINE" syntax
supported.  Could we just use that syntax and tell people using older
(I think probably much older) MySQL servers to upgrade?

Scott


On Mon, Apr 11, 2011 at 2:55 PM, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> 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>
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>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research