[Bioperl-l] Bio::Assembly tests failing

[Chris Fields]

Florent,

In the long run we're probably going to split some tests up so they're  
more module-specific (or parser-specific).  This is really a  
preemptive measure for the eventual bioperl split post-1.6, but we  
might as well tackle some of this now.

Thanks for taking care of that!

chris

On Nov 25, 2008, at 2:53 PM, Florent Angly wrote:

> Hi Chris,
>
> I didn't realize that there were Bio::Assembly related tests outside  
> of the t/Assembly.t file. The story is that I changed the ACE parser  
> so that it only gets its information from the ACE file (including  
> singlets). This was not the case before, so it broke the old, not  
> updated t/singlet.t tests. So what I did is to update and move the  
> tests that t/singlet.t did to t/Assembly.t and removed t/singlet.t.  
> All the Bio::Assembly tests should pass now.
> Cheers,
>
> Florent
>
>
> Chris Fields wrote:
>> I am getting tests failing on svn trunk (bioperl-live) that appear  
>> related to Bio::Assembly changes.  Florent, can you take a look at  
>> these?
>>
>> chris
>>
>> 1..4
>> ok 1 - use Bio::Assembly::IO;
>> ok 2 - Testing to see if the first contig is a Contig isa  
>> Bio::Assembly::Contig
>> not ok 3 - Testing to see if the first singlet is a Singlet isa  
>> Bio::Assembly::Singlet
>> not ok 4 - Testing to see if the Singlet ISA Contig isa  
>> Bio::Assembly::Contig
>>
>> #   Failed test 'Testing to see if the first singlet is a Singlet  
>> isa Bio::Assembly::Singlet'
>> #   at t/singlet.t line 25.
>> #     Testing to see if the first singlet is a Singlet isn't defined
>>
>> #   Failed test 'Testing to see if the Singlet ISA Contig isa  
>> Bio::Assembly::Contig'
>> #   at t/singlet.t line 27.
>> #     Testing to see if the Singlet ISA Contig isn't defined
>> # Looks like you failed 2 tests of 4.
>> Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 2/4 subtests
>>
>> Test Summary Report
>> -------------------
>> t/singlet.t (Wstat: 512 Tests: 4 Failed: 2)
>>  Failed tests:  3-4
>>  Non-zero exit status: 2
>> Files=1, Tests=4,  1 wallclock secs ( 0.01 usr  0.01 sys +  0.26  
>> cusr  0.04 csys =  0.32 CPU)
>> Result: FAIL
>> Failed 1/1 test programs. 2/4 subtests failed.
>>
>>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign