[Bioperl-l] tests failing badly

[Aaron J Mackey]

In fact, in reversing my changes to Bio::Factory::FTLocationFactory,
you've messed up things.  Here's what you have:

    $start =~ s/^\((.*)\)$/$1/;
    $end   =~ s/^\((.*)\)$/$1/ if $end;

This requires that start and end have *both* begin and end parentheses.
With this code, I get lots of:

Argument "202)" isn't numeric in numeric gt (>) at blib/lib/Bio/Location/Atomic.pm line 91, <GEN4> line 35.
Argument "(100" isn't numeric in numeric gt (>) at blib/lib/Bio/Location/Atomic.pm line 91, <GEN4> line 35.
Argument "202)" isn't numeric in numeric gt
[...]

With my patch:

    $start =~ s/^\(?(.*?)\)?/$1/;
    $end   =~ s/\(?(.*?)\)?$/$1/ if $end;

All tests pass cleanly.  What's the issue here?  Yes, when you mistakenly
set a Location's start to "202)" it turns into 202, but what's wrong with
having tests (and behavior) operate without spurious warnings?  Is this a
difference in your version of Perl and mine?

-Aaron

On Tue, 10 Sep 2002, Aaron J Mackey wrote:

>
> 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
> > -------------------------------------------------------------
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>
>

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu