[Bioperl-l] Bioperl-db install problems on macosx
Adam Witney
awitney at sghms.ac.uk
Wed Apr 9 22:28:19 EDT 2003
Ok, I have downloaded and installed 1.2.1 (not sure why the install
Bundle::BioPerl didn't do this earlier)
Just to be sure:
$ perldoc -m Bio::Ontology::Ontology | grep '$Id'
# $Id: Ontology.pm,v 1.2.2.4 2003/03/27 10:07:56 lapp Exp $
Now make test for bioperl-db gives some different errors
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.
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
....
t/map...............ok 2/6Can't locate object method "get_MapAdaptor" via
package "Bio::DB::BioSQL::DBAdaptor" (perhaps you forgot to load
"Bio::DB::BioSQL::DBAdaptor"?) at t/map.t line 28.
t/map...............dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-6
Failed 4/6 tests, 33.33% okay
t/marker............ok 4/19Can't locate object method "get_MapAdaptor" via
package "Bio::DB::BioSQL::DBAdaptor" (perhaps you forgot to load
"Bio::DB::BioSQL::DBAdaptor"?) at t/marker.t line 34.
t/marker............dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-19
Failed 15/19 tests, 21.05% okay
....
I have only implemented a PostgreSQL version of biosql... Is this failing
because markerdb is only in mysql currently?
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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