[BioSQL-l] biosql error on w2k/mySQL

[Wiepert, Mathieu]

Hi,

I am having a problem and I am not sure what it is.  I am guessing I am the only one trying this with win2k, but I have to give it a shot, at least for the moment (unless someone has biosql working with SqlServer 7?)

I have mySQL on windows 2000 server, it appears to be running, I have the schema loaded, but the tests seem to fail.  I have ActiveState perl for perl 5.6.  I followed Chirs Dagdigians doc, as well as the docs from the README in biosql-db.  I have DBI and DBD::mysql loaded, I ran the script to make the biosql db, and can view the tables.  However, when I run the tests, I get lots of failures.  So, I ran one test like this

C:\bioperl\bioperl-db>perl -I -w t/cluster.t
1..160
ok 1
ok 2
Undefined subroutine &Bio::Root::Root::throw called at D:/Perl/site/lib/Bio\DB\B
ioSQL\DBAdaptor.pm line 196, <GEN0> line 1.

(I tried nmake test_cluster TEST_VERBOSE=1, but got errors from nmake)

Most of the tests are like this, hitting the Root::throw problem (I must have something not installed correctly?)

I also ran the load_seqdatabase script and got this (modified the script to be more verbose)

C:\>perl -d:ptkdb c:\bioperl\bioperl-db\scripts\load_seqdatabase.pl -host PHARMG
KB -dbname biosql -dbuser root -format genbank C:\gbest1.seq
Loading C:\gbest1.seq ...
attempting to load adaptor class for Bio::Seq::RichSeq
        attempting to load module Bio::DB::BioSQL::RichSeqAdaptor
attempting to load adaptor class for Bio::Seq
        attempting to load module Bio::DB::BioSQL::SeqAdaptor
instantiating adaptor class Bio::DB::BioSQL::SeqAdaptor
attempting to load adaptor class for Bio::SeqFeature::Generic
        attempting to load module Bio::DB::BioSQL::GenericAdaptor
attempting to load adaptor class for Bio::Root::Root
        attempting to load module Bio::DB::BioSQL::RootAdaptor
Undefined subroutine &Bio::Root::Root::debug called at D:/Perl/site/lib/Bio/DB/B
ioSQL/BasePersistenceAdaptor.pm line 598, <GEN0> line 61.

I have the latest versions of bioperl-live, run, db, and biosql-schema.  BTW, I can't find any module called RichSeqAdaptor, does it exist?  

Thanks,

-Mat