[Bioperl-l] tests failing badly

[Hilmar Lapp]

I was able to track down and fix the problems with FTLocationFactory 
and EncodedSeq that caused some of the corresponding tests to fail.

Tests run clean now on my machine except for RepeatMasker. Shawn or 
someone from the Singapur guys, could you add the missing file?

	-hilmar

On Monday, September 9, 2002, at 05:57  PM, Hilmar Lapp wrote:

> I fixed PrimarySeq, some errors are still there:
>
> Failed Test         Stat Wstat Total Fail  Failed  List of Failed
> -------------------------------------------------------------------------------
> t/EncodedSeq.t       255 65280    31    0   0.00%
> t/LocationFactory.t              131    8   6.11%  13-15 21 23-25 31
> t/RepeatMasker.t       2   512     6    0   0.00%  ??
> Failed 3/105 test scripts, 97.14% okay. 7/4020 subtests failed, 
> 99.83% okay.
>
> EncodedSeq.t:
>
> t/EncodedSeq..............ok 32/31
> ------------- EXCEPTION  -------------
> MSG: Sequence is a protein. Cannot revcom
> STACK Bio::PrimarySeqI::revcom blib/lib/Bio/PrimarySeqI.pm:362
> STACK Bio::Seq::EncodedSeq::cds Bio/Seq/EncodedSeq.pm:476
> STACK toplevel t/EncodedSeq.t:74
>
> --------------------------------------
> t/EncodedSeq..............dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED test
>         Failed 0/31 tests, 100.00% okay
>
> RepeatMasker test is still failing due to a missing file (according 
> to Shawn).
>
> I'm going to investigate LocationFactory.t next. did anyone change 
> something there??
>
> 	-hilmar
>
> On Monday, September 9, 2002, at 05:32  PM, 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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>> Bioperl-l@bioperl.org
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>>
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------