Bug #44466 for bioperl-db: missing dependencies

Sat Mar 21 22:17:26 2009 allenday [...] cpan.org - Ticket created

Subject:

missing dependencies

I found these with the CentOS rpmbuild automatic perl dependency finder. None of this breaks the build. Some referenced modules aren't part of the distribution and can't be found on CPAN. Maybe they haven't been checked in or are no longer valid and should be removed: * scripts/corba/bioenv_server.pl references Bio::CorbaServer::BioENV * scripts/corba/caching_corba_server.pl references Bio::CorbaServer::BioEnv and Bio::CorbaClient::SeqDB Missing dependencies in Build.PL. I was able to find these on CPAN: * DBD::Oracle (referenced in Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver and Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver * CORBA::ORBit (referenced in scripts/corba/bioenv_server.pl, scripts/corba/test_bioenv.pl, and scripts/corba/caching_corba_server.pl)

Sat Mar 21 22:17:44 2009 allenday [...] cpan.org - Status changed from 'new' to 'open'

Thu Apr 16 13:31:40 2009 cjfields [...] uiuc.edu - Taken

Thu Apr 16 15:56:17 2009 cjfields [...] uiuc.edu - Correspondence added

On Sat Mar 21 22:17:26 2009, ALLENDAY wrote: Show quoted text

> I found these with the CentOS rpmbuild automatic perl dependency finder. > None of this breaks the build. > > Some referenced modules aren't part of the distribution and can't be > found on CPAN. Maybe they haven't been checked in or are no longer > valid and should be removed: > > * scripts/corba/bioenv_server.pl references Bio::CorbaServer::BioENV > * scripts/corba/caching_corba_server.pl references > Bio::CorbaServer::BioEnv and Bio::CorbaClient::SeqDB

I'll bring it up on the BioSQL list, but in all likelihood these will be removed. Show quoted text

> Missing dependencies in Build.PL. I was able to find these on CPAN: > > * DBD::Oracle (referenced in > Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver and > Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver > * CORBA::ORBit (referenced in scripts/corba/bioenv_server.pl, > scripts/corba/test_bioenv.pl, and scripts/corba/caching_corba_server.pl)

For the CORBA-related, see the above (i.e. it may be removed). The DBD adaptor isn't required unless one uses Oracle (same for DBD::mysql and DBD::Pg). We can maybe add it to recommends if one wants to install it.

Fri Jul 23 16:24:49 2010 cjfields [...] uiuc.edu - Correspondence added

On Thu Apr 16 15:56:17 2009, cjfields wrote: Show quoted text

> On Sat Mar 21 22:17:26 2009, ALLENDAY wrote:

> > I found these with the CentOS rpmbuild automatic perl dependency

> finder.

> > None of this breaks the build. > > > > Some referenced modules aren't part of the distribution and can't be > > found on CPAN. Maybe they haven't been checked in or are no longer > > valid and should be removed: > > > > * scripts/corba/bioenv_server.pl references Bio::CorbaServer::BioENV > > * scripts/corba/caching_corba_server.pl references > > Bio::CorbaServer::BioEnv and Bio::CorbaClient::SeqDB

> > I'll bring it up on the BioSQL list, but in all likelihood these will > be removed. >

> > Missing dependencies in Build.PL. I was able to find these on CPAN: > > > > * DBD::Oracle (referenced in > > Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver and > > Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver > > * CORBA::ORBit (referenced in scripts/corba/bioenv_server.pl, > > scripts/corba/test_bioenv.pl, and

> scripts/corba/caching_corba_server.pl) > > For the CORBA-related, see the above (i.e. it may be removed). > > The DBD adaptor isn't required unless one uses Oracle (same for > DBD::mysql and DBD::Pg). > We can maybe add it to recommends if one wants to install it.

The CORBA-based scripts are now gone. DBD::Oracle is not a dependency, but an optional driver (the modules in question are only used if DBD::Oracle is installed).

Fri Jul 23 16:24:50 2010 cjfields [...] uiuc.edu - Status changed from 'open' to 'resolved'