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

[Lincoln Stein]

The deprecation of TYPE=<engine> happened at mysql version 4.1, and so I am
checking using a select version() followed by either TYPE=MYISAM or
ENGINE=MYISAM. These changes are now committed.

Lincoln

On Mon, Apr 11, 2011 at 3:16 PM, Chris Fields <cjfields at illinois.edu> wrote:

> '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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


-- 
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>