[Bioperl-l] Assembly.t test fails

Chris Fields cjfields at uiuc.edu
Mon Apr 21 11:44:21 EDT 2008


Scratch that, figured it out (easy fix).

chris

On Apr 21, 2008, at 10:32 AM, Chris Fields wrote:

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





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