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

Jason Stajich jason at cgt.mc.duke.edu
Wed Apr 9 17:41:06 EDT 2003 

markerdb is old old and will go away or be reincarnated in a new form.
Ignore those msgs - I though the tests had been disabled - will make sure
that happens before we do a bioperl-biosql release.

I would probably just try and do a load - try the
scripts/biosql/load_seqdatabase.pl

-j

On Wed, 9 Apr 2003, Adam Witney wrote:

>
> 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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> >> believed to be clean.
> >>
> >> _______________________________________________
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> >>
>
>
>

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

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