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

[Adam Witney]

Hi Jason,

What should I be looking for? This just displays the pod for
Bio::Root::Root.

I initially had tested it against a manually built bioperl 1.2 but then
thinking I may be missing important modules just installed Bundle::BioPerl
from CPAN, which version is this currently?

Thanks for your help

adam

> 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


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