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

[Chris Fields]

Yes, go off master.

chris

On Apr 11, 2011, at 2:07 PM, Scott Cain wrote:

> Hi Lincoln,
> 
> I'm reasonably sure Chris said he is going to release off master.
> 
> Scott
> 
> 
> On Mon, Apr 11, 2011 at 3:06 PM, Lincoln Stein <lincoln.stein at gmail.com> wrote:
>> Hi Scott,
>> I'm fixing it now. What branch of bioperl is leading up to the release?
>> Lincoln
>> 
>> On Mon, Apr 11, 2011 at 3:02 PM, Scott Cain <scott at scottcain.net> 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
>> 
>> 
>> 
>> --
>> 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>
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> 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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