[Bioperl-l] bioperl-db make test errors

Dave Howorth dhoworth at mrc-lmb.cam.ac.uk
Fri Apr 16 06:12:09 EDT 2004

Hilmar Lapp wrote:
> To exclude the obvious:
>     - did you make sure that innodb is enabled in mysql? You have to 
> edit  the config file to do that. On the mysql prompt, insert a record 
> into  biodatabase, then issue a rollback. Is the record that you 
> inserted  still there?

Hi Hilmar,

Never underestimate the stupidity of the general public :)  I had 
modified the config file but forgotten to restart the server. Now it 
works. Thanks!

I was curious as to why I got no warnings when I created the database so 
I looked in the logs in case my memory was playing tricks. No warnings 
there either. So I RTFM and discovered that MySQL silently reverts to 
MyISAM if it isn't configured for the table type you request (for 
version < 4.1.1).

Perhaps it's worth adding your rollback test to the test suite or even 
to Bio::DB startup to protect fools against themselves? (I'll code the 
test if you wish).

Thanks again,
Dave Howorth
MRC Centre for Protein Engineering
Hills Road, Cambridge, CB2 2QH
01223 252960

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