[Bioperl-l] biosql error

[Hilmar Lapp]

If you upgraded perl you will need to recompile and re-install DBI as  
well as your DBD driver(s) of choice. What you're seeing is most likely  
not due to a bug - it rather looks like an installation issue on your  
machine.

Also, to see the DBI error messages, which in this case I'm pretty sure  
will conclusively point at the problem, supply --printerror to the  
script. (If your version doesn't recognize that option, you need to  
update from bioperl-db cvs.)

	-hilmar

On Monday, March 8, 2004, at 08:40  PM, 박준형 wrote:

> Dear Bioperl Experts
>
> I have some problem to perform biosql database update like this.
>
> Until upgrade perl 5.8.3, I had been used load_seqdatabase.pl script to
> update genbank file into biosql database.
>
> I don’t know what is the problem.
>
> Is there some method to fix these bugs?
>
>
>
> ------------- EXCEPTION  -------------
>
> MSG: failed to open connection:
>
> STACK Bio::DB::DBI::base::new_connection  
> /usr/local/lib/perl5/site_perl/5.8.
> 3//Bio/DB/DBI/base.pm:249
>
> STACK Bio::DB::DBI::base::get_connection  
> /usr/local/lib/perl5/site_perl/5.8.
> 3//Bio/DB/DBI/base.pm:209
>
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh
> /usr/local/lib/perl5/site_perl/5.8.3//Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.p
> m:1443
>
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::rollback
> /usr/local/lib/perl5/site_perl/5.8.3//Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.p
> m:1362
>
> STACK toplevel load_seqdatabase.pl:515
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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