[Bioperl-l] bioperl-db make test errors

[Dave Howorth]

I'm trying to set up bioperl-db and getting some errors in the make test 
  (full log is below). I just downloaded bioperl-db and biosql, and just 
upgraded mysql (from 3.23.49). MySQL appears to run OK with some 
existing databases. I just created a database (biosql_test) for the 
tests and loaded the biosqldb-mysql.sql schema.

I'm using:
bioperl 1.4
bioperl-db (the README says "README,v 1.17 2003/08/22 12:44:23")
biosql (the README says "README,v 1.4 2003/09/21 05:01:23")
Perl 5.6.1
MySQL 4.0.18
Debian woody with many backports

Does anybody have any idea what is causing the errors?

Cheers, Dave

----

bioperl-db$ make test
PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib 
-I/usr/lib/perl/5.6.1 -I/usr/share/perl/5.6.1 -e 'use Test::Harness 
qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
t/cluster.......ok 155/160 

-------------------- WARNING ---------------------
MSG: failed to store one or more child objects for an instance of class 
Bio::Cluster::UniGene (PK=1)
---------------------------------------------------
t/cluster.......ok 

t/comment.......ok 

t/dbadaptor.....ok 

t/dblink........ok 

t/ensembl.......ok 

t/fuzzy2........ok 

t/genbank.......ok 

t/locuslink.....NOK 24Can't call method "as_text" on an undefined value 
at t/locuslink.t line 122, <GEN0> line 1.
t/locuslink.....FAILED tests 24, 29-110 

	Failed 83/110 tests, 24.55% okay
t/ontology......ok 

t/query.........ok 

t/remove........ok 

t/seqfeature....ok 

t/simpleseq.....ok 

t/species.......ok 5/65 

------------- EXCEPTION  -------------
MSG: Unique key query in Bio::DB::BioSQL::SpeciesAdaptor returned 2 rows 
instead of 1. Query was [name_class="scientific name",binomial="Homo 
sapiens"]
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key 
blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:960
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key 
blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:856
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:183
STACK Bio::DB::Persistent::PersistentObject::create 
blib/lib/Bio/DB/Persistent/PersistentObject.pm:243
STACK toplevel t/species.t:35

--------------------------------------
t/species.......dubious 

	Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 6-65
	Failed 60/65 tests, 7.69% okay
t/swiss.........ok 

Failed Test   Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/locuslink.t              110   83  75.45%  24 29-110
t/species.t    255 65280    65  120 184.62%  6-65
Failed 2/15 test scripts, 86.67% okay. 143/930 subtests failed, 84.62% okay.
make: *** [test_dynamic] Error 11