[Bioperl-l] error installing bioperl-db

Hilmar Lapp hlapp at gmx.net
Tue Jul 26 16:20:07 EDT 2005

I fixed this. Should propagate to anonymous cvs within the next hours, 
the new version of the module will be 1.3. I tested against an 
PostgreSQL 8.0.3 server and all tests pass.

For the curious, the problem was that DBD::Pg binds all parameters as 
type VARCHAR by default, and does use 'real' prepared statements by 
default if the server is 8.x but not if it's 7.3.x. This is why the 
problem only surfaces when using an 8.x server. The server apparently 
doesn't like VARCHAR-type parameters bound to the SUBSTRING arguments, 
so what I did was explicitly specify the type as integer to the 
$sth->bind_param() call.


On Jul 26, 2005, at 6:50 AM, Andrew Stewart wrote:

> I updated BiosequenceAdaptorDriver.pm to 1.2. Here's the first 
> erroneous bit of the make test. Looks like the same thing?
> -Andrew
> preparing SELECT statement: SELECT SUBSTRING(seq FROM ? FOR ?) FROM 
> biosequence WHERE bioentry_id = ?
> ok 30
> ok 31
> DBD::Pg::st execute failed: ERROR: invalid escape string
> HINT: Escape string must be empty or one character.
> CONTEXT: SQL function "substring" statement 1
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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