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

[Scott Cain]

Hi Lincoln,

I made a minor modification to this so that it wouldn't complain about
version numbers like 5.5.9:

  https://github.com/bioperl/bioperl-live/commit/5ff758a1a8efc5f43521e6ade3bf62e724b98dcb

Scott


On Monday, April 11, 2011, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> 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/)                     --
> 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