[Bioperl-l] 1.1.1 progress

[Hilmar Lapp]

> -----Original Message-----
> From: Ewan Birney [mailto:birney@ebi.ac.uk]
> Sent: Tuesday, October 08, 2002 2:18 AM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] 1.1.1 progress
> 
> 
> 
> 
> Well... I knew it wasn't going to be easy.
> 
> 
> I am currently bug fixing against 5.0005
> 
> Summary of my perl5 (5.0 patchlevel 5 subversion 3) configuration:
> 
> 
> I have delt with two big ones 
> 
>   (a) using "our" in the primaryseq module (changed to "my" - 
> is this ok 
> hilmar?)
> 

Should be OK.

> 
>   (b) building a work around for flush for 5.005 etc. Now 
> Bio::Root::IO
> has a method "flush" which should "do the right thing".
> 
> 
> 
> 
> 
> I am working on:
> 
> 
> 
> Failed Test  Status Wstat Total Fail  Failed  List of failed
> --------------------------------------------------------------
> -----------------
> t/BPlite.t      255 65280    97   96  98.97%  2-97
> t/CoordinateMap   2   512   147  147 100.00%  1-147
> t/EncodedSeq.t  255 65280    37   37 100.00%  1-37
> t/Index.t         0    11    12   12 100.00%  1-12
> t/RandomTreeFac 255 65280     4    2  50.00%  3-4
> t/TreeIO.t      255 65280    17   13  76.47%  5-17
> t/UniGene.t                  42   14  33.33%  3-8, 11, 16-21, 23
> t/flat.t        255 65280     7    3  42.86%  5-7
> 

Geezz... We haven't been testing on 5.005 for quite a while ...

> 
> 
> Some of which will be trivial, some hard. Given Hilmar's 
> recent posts I 
> would also like to ensure that aliases for the old method calls on 
> SeqFeatureI are there (Hilmar - if you don't get around to 
> this, I will 
> get around to it ;)).
> 

I did put in aliases. Blame me where I forgot :-)

I actually started gathering them at the bottom of a module (SeqFeature::Generic) so that it is easier to keep track of them and switch to (or switch off) deprecation warnings if desired.

	-hilmar