[Bioperl-l] Bioperl-db install problems on macosx

[Adam Witney]

Hi,

Has anyone managed to get bioperl-db installed on macosx? Most of the tests
fail on my 10.2.4 machine (perl 5.6.1)

The errors are quite extensive but it starts off...

[mrc1-003:local/install/bioperl-db] adam% make test
PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib
-I/System/Library/Perl/darwin -I/System/Library/Perl -e 'use Test::Harness
qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
t/cluster...........ok 2/160
------------- EXCEPTION  -------------
MSG: failed to load adaptor for class Bio::Cluster::UniGene as well as
parents Bio::Root::Root, Bio::Cluster::UniGeneI, Bio::IdentifiableI,
Bio::DescribableI, Bio::AnnotatableI, Bio::Factory::SequenceStreamI
STACK Bio::DB::BioSQL::DBAdaptor::_get_object_adaptor_class
blib/lib/Bio/DB/BioSQL/DBAdaptor.pm:196
STACK Bio::DB::BioSQL::DBAdaptor::get_object_adaptor
blib/lib/Bio/DB/BioSQL/DBAdaptor.pm:100
STACK Bio::DB::BioSQL::DBAdaptor::create_persistent
blib/lib/Bio/DB/BioSQL/DBAdaptor.pm:261
STACK toplevel t/cluster.t:30

--------------------------------------
t/cluster...........dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 3-160
        Failed 158/160 tests, 1.25% okay
t/comment...........ok 2/11Use of uninitialized value in string eq at
blib/lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm line 342, <GEN0> line 72.
Use of uninitialized value in string eq at
blib/lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm line 342, <GEN0> line 72.
Use of uninitialized value in string eq at
blib/lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm line 342, <GEN0> line 72.
Use of uninitialized value in string eq at
blib/lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm line 342, <GEN0> line 72.
Use of uninitialized value in string eq at
blib/lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm line 342, <GEN0> line 72.
Use of uninitialized value in string eq at
blib/lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm line 342, <GEN0> line 72.
Use of uninitialized value in string eq at
blib/lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm line 342, <GEN0> line 72.
Use of uninitialized value in string eq at
blib/lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm line 342, <GEN0> line 72.
Use of uninitialized value in string eq at
blib/lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm line 342, <GEN0> line 72.
Use of uninitialized value in string eq at
blib/lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm line 342, <GEN0> line 72.
Use of uninitialized value in string eq at
blib/lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm line 342, <GEN0> line 72.
Use of uninitialized value in string eq at
blib/lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm line 342, <GEN0> line 72.
Can't locate object method "new" via package "Bio::Ontology::Ontology"
(perhaps you forgot to load "Bio::Ontology::Ontology"?) at
blib/lib/Bio/DB/BioSQL/SeqFeatureAdaptor.pm line 669, <GEN0> line 72.
t/comment...........dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 3-11
        Failed 9/11 tests, 18.18% okay


.... And then continues with lots more of these "Use of uninitialized value"
messages for each test...

Thanks for any help

adam


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