[Bioperl-l] Bioperl-db make test failures

Hilmar Lapp hlapp at gnf.org
Wed Feb 11 15:00:30 EST 2004

That explains the species test failure. It tests, among other things, 
whether it can successfully insert a species. As it is not a made up 
taxon, it'll fail if you pre-loaded the ncbi taxon database.

Generally, I recommend creating a test schema for test scripts that's 
separate from the instance you use for production or anything else that 
you don't want to throw away in an instant and not be sorry.


On Wednesday, February 11, 2004, at 11:39  AM, Adam Witney wrote:

> On 11/2/04 7:18 pm, "Hilmar Lapp" <hlapp at gnf.org> wrote:
>> This is strange, actually both of them. Did you run the tests against 
>> a
>> database with content loaded prior to the tests, or was it a freshly
>> created instance of the schema?
>> If the latter, which RDBMS, and version of bioperl are you using?
> I had created the database and only run load_ncbi_taxonomy.pl to 
> download
> the taxonomy database from NCBI
> Both biosql-schema and bioper-db were downloaded from CVS yesterday. 
> is PostgreSQL 7.4.1
> Thanks
> adam
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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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