[Bioperl-l] [Gmod-gbrowse] Fwd: DB::SeqFeature::Store error

[Scott Cain]

Hi Chris,

I think adding the type=MYISAM is the right thing to do; please go ahead
and commit it.

Scott



On Mon, 2007-10-01 at 10:14 -0500, Chris Fields wrote:
> Just thought I would forward this on to the GBrowse list as well in  
> case anyone has run into the same problem.  The issue pops up when  
> using bioperl from CVS and appears to be related to a fix Lincoln  
> added recently in Bio::DB::SeqFeature::Store::DBI::mysql using  
> FULLTEXT, which only works for MyISAM currently.
> 
> Making the suggested changes (adding TYPE=MYISAM) to the CREATE TABLE  
> queries does work when InnoDB is set to the default.  Should I go  
> ahead and commit?
> 
> chris
> 
> Begin forwarded message:
> 
> > I'm getting the following error on my local MySQL (v 5.0.41) with
> > bp_seqfeature_load:
> >
> > -------------------- EXCEPTION --------------------
> > MSG: The used table type doesn't support FULLTEXT indexes
> > STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database /Library/
> > Perl/5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:414
> > STACK Bio::DB::SeqFeature::Store::init_database /Library/Perl/5.8.6/
> > Bio/DB/SeqFeature/Store.pm:382
> > STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /Library/Perl/
> > 5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:218
> > STACK Bio::DB::SeqFeature::Store::new /Library/Perl/5.8.6/Bio/DB/
> > SeqFeature/Store.pm:345
> > STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:57
> > -------------------------------------------
> >
> > The default setting for storage is InnoDB; switching to MyISAM fixes
> > the issue.  Should we specify TYPE = MyISAM with the various CREATE
> > TABLE queries in Bio::DB::SeqFeature::Store::DBI::mysql to be on the
> > safe side?
> >
> > chris
> 
> 
> 
> 
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory