[Bioperl-l] Bioperl-db make test failures
awitney at sghms.ac.uk
Wed Feb 11 15:07:01 EST 2004
I installed the bioperl-db module anyway, but when I tried to load a GenBank
file into the database, the same species failure came up... Should I not
load the ncbi taxon database?
> 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
>>> 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
>> the taxonomy database from NCBI
>> Both biosql-schema and bioper-db were downloaded from CVS yesterday.
>> is PostgreSQL 7.4.1
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