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

[Scott Cain]

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