[Biojava-l] Re: BioSQL Installation Error

[Thomas Down]

On Fri, Apr 25, 2003 at 12:29:01PM +0100, Y D Sun wrote:
> Dear Thomas,
> 
> I am trying to install BioSQL on PostgreSQL 7.3.2 and RedHat 7.3. I have
> successfully run biosqldb-pg.sql and biosqldb-assembly-pg.sql, but
> failed when running biosql-accelerators-pg.sql with the following
> errors:
> 
> psql:/addon/local/biosql/biosql-accelerators-pg.sql:4: ERROR:
> RemoveFunction: function biosql_accelerators_level() does not exist
> psql:/addon/local/biosql/biosql-accelerators-pg.sql:10: ERROR:  language
> "plpgsql" does not exist
> psql:/addon/local/biosql/biosql-accelerators-pg.sql:12: ERROR:
> RemoveFunction: function intern_ontology_term(text) does not exist
> psql:/addon/local/biosql/biosql-accelerators-pg.sql:26: ERROR:  language
> "plpgsql" does not exist
> psql:/addon/local/biosql/biosql-accelerators-pg.sql:28: ERROR:
> RemoveFunction: function intern_seqfeature_source(text) does not exist
> psql:/addon/local/biosql/biosql-accelerators-pg.sql:42: ERROR:  language
> "plpgsql" does not exist
> psql:/addon/local/biosql/biosql-accelerators-pg.sql:45: ERROR:
> RemoveFunction: function create_seqfeature(integer, text, text) does not
> exist
> psql:/addon/local/biosql/biosql-accelerators-pg.sql:59: ERROR:  language
> "plpgsql" does not exist
> psql:/addon/local/biosql/biosql-accelerators-pg.sql:61: ERROR:
> RemoveFunction: function create_seqfeature_onespan(integer, text, text,
> integer, integer, integer) does not exist
> psql:/addon/local/biosql/biosql-accelerators-pg.sql:85: ERROR:  language
> "plpgsql" does not exist

Note that the accelerators code isn't vital to using BioSQL --
although it can give significant improvements to write performance.

The RemoveFunction arrors aren't a problem, these are just
warning messages.  The accelerators file contains DROP FUNCTION
statements so that if you re-run the accelerators file, the old
proceedures are replaced.

> According to the tutorial "Installing and using BioSQL",I have enabled
> the pgsql language as:
> 
> createlang -L .../lib plpgsql template1

That looks like the correct solution to me.  Did you do this
before or after creating the database you are using for the
BioSQL schema?  If you ran this afterwards, try creating a
new database.

Did you get any error messages from the createlang command?

     Thomas.