[Bioperl-l] tests failing badly

Aaron J Mackey Aaron J. Mackey" <amackey@virginia.edu
Tue, 10 Sep 2002 00:19:43 -0400 (EDT)


Remember that some of us quit working after 5 pm EDT; that means that if
you've found a problem with something I've committed, maybe you can just
ask me to fix it?

In the development of Bio::Seq::EncodedSeq, I found that repeatedly when I
reset the seq() of an object, that PrimarySeq was "guessing" my alphabet,
and setting it to protein; I apologize greatly for not making sure
everything else tested out OK (but, in fact, all tests ran cleanly here).
But whatever you've changed seems to have introduced a myriad of warnings,
and now EncodedSeq seems to think it's a protein sometimes ...

I'm now working on cleaning things up, because indeed I now have make test
issues ...

mea culpa, mea culpa,

-Aaron

On Mon, 9 Sep 2002, Hilmar Lapp wrote:

> I just did a cvs update ...
>
> Failed Test         Stat Wstat Total Fail  Failed  List of Failed
> -------------------------------------------------------------------------------
> t/AlignStats.t       255 65280    15   11  73.33%  2-3 7-15
> t/EncodedSeq.t                    31   ??       %  ??
> t/LocationFactory.t              131    8   6.11%  13-15 21 23-25 31
> t/RepeatMasker.t       2   512     6    0   0.00%  ??
> t/SeqAnal.t          255 65280     1    1 100.00%  1
> t/Tools.t            255 65280     8    4  50.00%  5-8
> Failed 6/105 test scripts, 94.29% okay. 18/4020 subtests failed,
> 99.55% okay.
>
> Many of which have to do with alphabet setting ... I'm going to
> investigate as I need to have this working.
>
> 	-hilmar
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
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-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu