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

[Lincoln Stein]

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>