[Bioperl-l] Biosql schema for use w/ bioperl-1.2.1

[Steve Mathias]

>>>>> "Hilmar" == Hilmar Lapp <hlapp at gnf.org> writes:

Hilmar> You need the latest CVS HEAD revision from both biosql-schema
Hilmar> and bioperl-db. Earlier versions of biosql-schema will not work
Hilmar> with the latest bioperl-db. It sounds like you're not running
Hilmar> the latest bioperl-db? Is NP_000358 the first entry in your
Hilmar> input file? There should have been some DBI-generated noise
Hilmar> preceding that stack trace.

Hilmar> did bioperl-db pass all tests? Specifically, what's the output
Hilmar> for

Hilmar> $ make test_species TEST_VERBOSE=1

Hilmar> If any one of those tests fails, please do

Hilmar> $ setenv HARNESS_VERBOSE 1 # csh, tcsh or $ export
Hilmar> HARNESS_VERBOSE=1 # ksh, bash

Hilmar> then run the above command again and send me the output.

Here it is:

smathias at poblano 1226 > make test_species TEST_VERBOSE=1
PERL_DL_NONLAZY=1 /usr/local/bin/perl -Iblib/arch -Iblib/lib -I/usr/local/lib/perl5/5.6.1/i686-linux -I/usr/local/lib/perl5/5.6.1 -e 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests @ARGV;' t/species.t
t/species....1..65
ok 1
ok 2
attempting to load adaptor class for Bio::Species
        attempting to load module Bio::DB::BioSQL::SpeciesAdaptor
instantiating adaptor class Bio::DB::BioSQL::SpeciesAdaptor
ok 3
ok 4
ok 5
attempting to load driver for adaptor class Bio::DB::BioSQL::SpeciesAdaptor
Using Bio::DB::BioSQL::mysql::SpeciesAdaptorDriver as driver peer for Bio::DB::BioSQL::SpeciesAdaptor
preparing UK select statement: SELECT taxon_name.taxon_id, NULL, NULL, taxon.ncbi_taxon_id, taxon_name.name, NULL FROM taxon, taxon_name WHERE taxon.taxon_id = taxon_name.taxon_id AND name_class = ? AND name = ?
SpeciesAdaptor: binding UK column 1 to "scientific name" (name_class)
SpeciesAdaptor: binding UK column 2 to "Homo sapiens" (binomial)
DBD::mysql::st execute failed: Table 'biosql.taxon_name' doesn't exist at blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 892.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: error while executing statement in Bio::DB::BioSQL::SpeciesAdaptor::find_by_unique_key: Table 'biosql.taxon_name' doesn't exist
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm:342
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:898
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:809
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:180
STACK: Bio::DB::Persistent::PersistentObject::create blib/lib/Bio/DB/Persistent/PersistentObject.pm:242
STACK: t/species.t:35
-----------------------------------------------------------
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 6-65
        Failed 60/65 tests, 7.69% okay
Failed Test Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/species.t  255 65280    65   60  92.31%  6-65
Failed 1/1 test scripts, 0.00% okay. 60/65 subtests failed, 7.69% okay.
make: *** [test_species] Error 2


-- 
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Steve Mathias                         email: smathias at unm.edu
UNM Office of Biocomputing              phone: (505) 272-8111
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