[Bioperl-l] Bio::Assembly tests failing
cjfields at illinois.edu
Wed Nov 26 09:31:13 EST 2008
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!
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.
> 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
>> ok 1 - use Bio::Assembly::IO;
>> ok 2 - Testing to see if the first contig is a Contig isa
>> not ok 3 - Testing to see if the first singlet is a Singlet isa
>> not ok 4 - Testing to see if the Singlet ISA Contig isa
>> # 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
>> # 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.
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign
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