[InterMine Dev] bioseg error message

Kalpana Karra kkarra at stanford.edu
Tue Nov 24 19:00:44 GMT 2009


It looks like we did have problems with bioseg installation.

Before:
template1=# select bioseg_create(1,2);
ERROR:  function bioseg_create(integer, integer) does not exist
LINE 1: select bioseg_create(1,2);
                ^
HINT:  No function matches the given name and argument types. You  
might need to add explicit type casts.


Our sysadmin has fixed the problem.. this is the note from him..

>  There is an issue with the bioseg.so shared library -- it's the  
> wrong version from the server, so I have to rebuild it.


After:
template1=# select bioseg_create(1,2);
  bioseg_create
---------------
  1..2
(1 row)

It seem to work. I will have to redo the MalariaMine build to make  
sure it will now work without errors.

Will keep you all posted.

Thanks,
-Kalpana



On Nov 2
4, 2009, at 10:31 AM, Matthew Wakeling wrote:

> On Tue, 24 Nov 2009, Kalpana Karra wrote:
>> We did install bioseg in template1 before trying the build.  This  
>> is odd.
>
> Please could you let me know the results of the test that Julie sent  
> you:
>
>> You can verify bioseg is installed correctly by running this in the  
>> postgres database:
>>
>>      select bioseg_create(1,2);
>
> If the above test returns an error for the production database, then  
> bioseg is not correctly installed. The final step of the install may  
> have been missed out, which is:
>
> psql production <bioseg.sql
> psql production <btree_gist.sql
>
> while you are in the postgres contrib directory (which on Debian is / 
> usr/share/postgresql/<version number>/contrib)
>
> Matthew
>
> -- 
> People who love sausages, respect the law, and work with IT  
> standards shouldn't watch any of them being made.  -- Peter Gutmann




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