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

[Hilmar Lapp]

On Wednesday, April 9, 2003, at 10:31  AM, Adam Witney wrote:

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

He meant the version number. If you say

	$ perldoc -m Bio::Ontology::Ontology | grep '$Id'

you should see

# $Id: Ontology.pm,v 1.2.2.4 2003/03/27 10:07:56 lapp Exp $

If not, you don't run bioperl 1.2.1.

	-hilmar


>
> 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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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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