[Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0

[Chris Fields]

Okay, wasn't able to reproduce this using my Ubuntu8.10/perl5.10  
setup.  I'm wondering if it's a permissions issue; I was able to  
reproduce this on portal.open-bio.org:

t/LocalDB/Registry...........................
--------------------- WARNING ---------------------
MSG: Couldn't call new_from_registry() on [Bio::DB::Flat]

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: you must specify an indexing scheme
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160
STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252
STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164
STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95
STACK: t/LocalDB/Registry.t:51
-----------------------------------------------------------

---------------------------------------------------
ok

chris

On Jan 26, 2009, at 7:24 AM, Chad Davis wrote:

> Strangely enough, I don't get that Bio::DB::Registry error on CentOS
> 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still
> get it on Ubuntu 8.10(i686)/Perl 5.10.0.
>
> Chad
>
> On Mon, Jan 26, 2009 at 12:52, Dave Messina  
> <David.Messina at sbc.su.se> wrote:
>> Thanks so much, Chris and everyone else, for your hard work on this  
>> release.
>>
>> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing  
>> that weire
>> Bio::DBRegistry warning:
>>
>> t/LocalDB/Registry.............................3/14
>> --------------------- WARNING ---------------------
>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat]
>>
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: you must specify an indexing scheme
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160
>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252
>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164
>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95
>> STACK: t/LocalDB/Registry.t:51
>> -----------------------------------------------------------
>>
>> ---------------------------------------------------
>> t/LocalDB/Registry.............................ok
>>
>>
>>
>> This may simply be something funky in my local environment since no  
>> one else
>> has corroborated, though.
>>
>>
>> Dave
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
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