[Bioperl-l] bioperl-db failing tests

Michael Muratet US-Huntsville Michael.Muratet at operon.com
Tue Jun 6 14:34:38 EDT 2006


I am trying to install bioperl-db in preparation for installing a biosql database. I'm running on a Dell PowerEdge with quad dual-core Xeons and RedHat Enterprise v4 and perl 5.8.5 and bioperl 1.5.1.  I have installed mysql v5.0.21 from source with --with-innodb set for the configuration. I installed bioperl-db from cvs. I have the latest DBI and DBD:mysql installed a few weeks ago from CPAN. The installation has been working well with perl otherwise, for example, the Ensembl core API works OK. SHOW ENGINES indicates that innodb is enabled.  I have attached a snippet from the top of the output below. I searched the web and the bioperl-db list and haven't found anything that appears to be relevant. I've done several of these installs and they've pretty much completed without a single glitch. Does anyone have any ideas how to isolate the problem?



[mmuratet at HSV-PROBE bioperl-db]$ make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01dbadaptor.....ok 14/19
------------- EXCEPTION  -------------
MSG: failed to open connection: Transactions not supported by database
STACK Bio::DB::DBI::base::new_connection /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:255
STACK Bio::DB::DBI::base::get_connection /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/DBI/base.pm:215
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1477
STACK Bio::DB::BioSQL::BaseDriver::prepare_findbyuk_sth /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/BioSQL/BaseDriver.pm:518
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:927
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/lib/perl5/site_perl/5.8.5/Bio/biosql-schema/sql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
STACK toplevel t/01dbadaptor.t:62

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