[Bioperl-l] Bio::Assembly tests failing

[Florent Angly]

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.
>
>