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

[Scott Cain]

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