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

[Chris Fields]

'show engines' gives a list with the default noted.

http://dev.mysql.com/doc/refman/5.1/en/storage-engines.html

Not sure if this available for older versions, but it looks as if it goes back to at least v 4.1 :)

chris

On Apr 11, 2011, at 2:02 PM, Scott Cain wrote:

> Or, much better, perhaps there is a way to change the default engine
> via a query, so it could be set to myisam before the table creation
> starts.
> 
> Scott
> 
> 
> On Mon, Apr 11, 2011 at 3:00 PM, Scott Cain <scott at scottcain.net> wrote:
>> 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>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> 
>> 
>> 
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
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