[BioSQL-l] latest versions for bioperl-db biosql-schema ?

[Kris Boulez]

Quoting Kris Boulez (kris.boulez at algonomics.com):
> Quoting Hilmar Lapp (hlapp at gnf.org):
> > I've fixed this now. This was essentially the hash sort order problem 
> > that changes in perl 5.8 and bit many people already. I added a 
> > function that introduces an explicit sort order following the 
> > inheritance tree (depth-first).
> > 
> 
> The problem with the comment.t test seems fixed. Stay tuned for more
> errors (5/18 tests fail).
> 

As promised, here are some more warnings/errors from running make test.
A best effort for locating the problem is given.


dblink.t (and ensembl.t, fuzzy2.t genbank.t)
-------- 
a message is printed like

  DBD::mysql::st bind_param failed: Illegal parameter number at
  blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1081, <GEN0>
  line 72.

This seems to come from the following evaled code

      eval { $rv = $sth->bind_param($i, $qvalues->[$i-1]); };

(return value is checked, but DBD::mysql is chatty)


ePCRdb.t
--------
The third test (of three) fails with

  Can't locate object method "get_MapAdaptor" via package
  "Bio::DB::BioSQL::DBAdaptor" at t/ePCRdb.t line 29.

The code in question is

  my $mapadaptor = $db->get_MapAdaptor();

get_Mapadaptor() is defined in Bio/DB/Map/DBAdaptor.pm




locuslink.t
-----------
An exception is thrown after test 4

  ------------- EXCEPTION Bio::Root::NotImplemented -------------
  MSG: Abstract method "Bio::Ontology::TermI::get_dblinks" is not
  implemented by package Bio::Annotation::OntologyTerm.
  This is not your fault - author of Bio::Annotation::OntologyTerm
  should be blamed!

Perhaps I need the latest code from bioperl-live cvs ?



remove.t
--------
Gives multiple warnings (again from DBD::mysql) like

  DBD::mysql::st execute failed: Duplicate entry '1-1-1' for key 1 at
  blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 401, <GEN0> line
  282.
  DBD::mysql::st execute failed: Duplicate entry '1-2-2' for key 1 at
  blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 401, <GEN0> line
  282.
  DBD::mysql::st execute failed: Duplicate entry '1-3-3' for key 1 at
  blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 401, <GEN0> line
  282.

This is for the code starting around line 90 of remove.t ("test
removing associations").