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

[Jason Stajich]

you do have bioperl 1.2.1 installed, right?...

Doesn't look like it.
% perldoc Bio::Root::Root

should present you with something.



On Wed, 9 Apr 2003, Adam Witney wrote:

> 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
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu