[Bioperl-l] Assembly.t test fails

Chris Fields cjfields at uiuc.edu
Mon Apr 21 11:32:59 EDT 2008


I'm getting some significant test failures in bioperl-live for  
Bio::Assembly:

t/Assembly......
1..35
ok 1 - use Bio::Assembly::IO;
ok 2 - The object isa Bio::Assembly::IO
ok 3 - The object isa Bio::Assembly::Scaffold
ok 4
not ok 5
ok 6 - The object isa Bio::AnnotationCollectionI
ok 7 - no annotations in Annotation collection?
ok 8

#   Failed test at t/Assembly.t line 35.
#          got: 'NoName'
#     expected: 'test'
Can't locate object method "get_contig_seq_ids" via package  
"Bio::Assembly::Contig" at /Users/cjfields/bioperl/bioperl-live/blib/ 
lib/Bio/Assembly/Scaffold.pm line 189, <GEN0> line 733.
# Looks like you planned 35 tests but only ran 8.
# Looks like you failed 1 test of 8 run.
# Looks like your test died just after 8.
  Dubious, test returned 255 (wstat 65280, 0xff00)
  Failed 28/35 subtests

Test Summary Report
-------------------
t/Assembly.t (Wstat: 65280 Tests: 8 Failed: 1)
   Failed test:  5
   Non-zero exit status: 255
   Parse errors: Bad plan.  You planned 35 tests but ran 8.
Files=1, Tests=8,  0 wallclock secs ( 0.01 usr  0.00 sys +  0.22 cusr   
0.04 csys =  0.27 CPU)
Result: FAIL
Failed 1/1 test programs. 1/8 subtests failed.


chris

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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