[BioSQL-l] BIOSQL on Oracle 10.1.0.3 needs an Oracle Patch

Gerben Menschaert Gerben.Menschaert at UGent.be
Mon Apr 24 13:43:12 UTC 2006


Hello,

Just for you information...

If you're installing BIOSQL on Oracle 10.1.0.3 on Linux AS 2.1, you need to
install the Oracle patch 3612581 (can be found on
http://metalink.oracle.com). If not you will run into the following error,
while testing the bioperl-db installation:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: error while executing statement in
Bio::DB::BioSQL::PrimarySeqAdaptor::find_by_unique_key: ORA-00600: internal
error code, arguments: [kpofdr-long], [], [], [], [], [], [], [] (DBD ERROR:
error possibly near <*> indicator at char 138 in 'SELECT bioentry.oid,
bioentry.name, bioentry.identifier, bioentry.accession,
bioentry.description, bioentry.version, bioentry.db_oid FROM <*>bioentry
WHERE db_oid = :p1 AND accession = :p2')
STACK: Error::throw
STACK: Bio::Root::Root::throw /src/bioperl/bioperl-live/Bio/Root/Root.pm:328
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
/src/bioperl/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:951
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
/src/bioperl/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
STACK: t/03simpleseq.t:88
-----------------------------------------------------------
t/03simpleseq.....FAILED tests 29-59

        Failed 31/59 tests, 47.46% okay

If the patch is installed all tests are successful.


I'm running perl v.5.8.0, Bioperl version 1.5.1 from CVS HEAD, Bioperl-db
CVS HEAD, working on Biosql installed on Oracle 10.1.0.3 on Linux 2.1. AS.


Regs,
Gerben Menschaert




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