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

Hilmar Lapp hlapp at gnf.org
Wed Apr 9 16:26:19 EDT 2003 

On Wednesday, April 9, 2003, at 01:28  PM, Adam Witney wrote:

>
> Lots of these throughout:
>
> Use of uninitialized value in string eq at
> blib/lib/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm line 342, <GEN0> 
> line 72.

This is harmless. I've fixed the statement though that led to the 
warning, but it should be doing the right thing.

>
> And several tests fail like so:
>
> ....
> t/ePCRdb............ok 2/3Can't locate object method "get_MapAdaptor" 
> via
> package "Bio::DB::BioSQL::DBAdaptor" (perhaps you forgot to load
> "Bio::DB::BioSQL::DBAdaptor"?) at t/ePCRdb.t line 29.
> t/ePCRdb............dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED test 3
>         Failed 1/3 tests, 66.67% okay
>

This is due to a misconfiguration in DBHarness.markerdb.conf. Make sure 
key database has the value 'map' for markerdb:

     # The name of the database within bioperl-db (biosql or map)
     'database'      => 'map',

Also, markerdb is not supported on Pg yet, so the driver in this file 
needs to be mysql:

     # DBD driver to use - mandatory
     'driver'        => 'mysql',

(Note that this is not true for DBHarness.biosql.conf!)

This will also fix the other 2 markerdb tests.


> I have only implemented a PostgreSQL version of biosql... Is this 
> failing
> because markerdb is only in mysql currently?
>

See above.

	-hilmar



> Thanks for any help
>
> adam
>
>>
>> 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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