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

[Chris Fields]

Done.  If we run into issues and need to roll back let me know.

chris

On Oct 4, 2007, at 10:08 AM, Scott Cain wrote:

> 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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> -- 
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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
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign