[Bioperl-l] t/FeatureHolder.x

Sendu Bala bix at sendu.me.uk
Mon Feb 19 12:42:23 EST 2007


Is this supposed to work? It doesn't get run in the test suite normally 
because of its name.

With a live checkout I get:
./Build test --test_files t/FeatureHolder.x --verbose
t/FeatureHolder....1..6
ok 1
ok 2
Set group tag to: locus_tag
GROUPS:
   GROUP [?]:source

[snip]

   resolved pair Bio::SeqFeature::Generic=HASH(0x1375dc0) 
Bio::SeqFeature::Generic=HASH(0x1362830)
UNFLATTENING GROUP:
   GROUP [?]:gene
UNFLATTENING GROUP:
   GROUP [?]:repeat_region
UNFLATTENING GROUP:
   GROUP [?]:gene
UNFLATTENING GROUP:
   GROUP [?]:repeat_region
UNFLATTENING GROUP:
   GROUP [BG:DS07721.3]:gene mRNA CDS
UNFLATTENING GROUP:
   GROUP [BG:DS07721.6]:gene mRNA CDS

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: DUPLICATE ID: AAF53399.1
STACK: Error::throw
STACK: Bio::Root::Root::throw 
/home/sendu/src/bioperl/core/blib/lib/Bio/Root/Root.pm:359
STACK: 
Bio::SeqFeature::Tools::IDHandler::create_hierarchy_from_ParentIDs 
/home/sendu/src/bioperl/core/blib/lib/Bio/SeqFeature/Tools/IDHandler.pm:175
STACK: Bio::FeatureHolderI::create_hierarchy_from_ParentIDs 
/home/sendu/src/bioperl/core/blib/lib/Bio/FeatureHolderI.pm:245
STACK: t/FeatureHolder.x:68
-----------------------------------------------------------
dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-6
         Failed 4/6 tests, 33.33% okay
Failed Test       Stat Wstat Total Fail  List of Failed
-------------------------------------------------------------------------------
t/FeatureHolder.x  255 65280     6    8  3-6
Failed 1/1 test scripts. 4/6 subtests failed.
Files=1, Tests=6,  1 wallclock secs ( 0.55 cusr +  0.04 csys =  0.59 CPU)
Failed 1/1 test programs. 4/6 subtests failed.


It also fails quite differently with 1.5.2.


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