[Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0

[Chris Fields]

Okay, committed that to trunk.  Oddly BerkeleyDB didn't show up as a  
dependency for that module; will have to look into that.

chris

On Jan 26, 2009, at 11:08 AM, Chad Davis wrote:

> It seems to be a dependency issue. This fixed it:
>
> --- t/LocalDB/Registry.t.bak	2009-01-25 06:19:15.000000000 +0100
> +++ t/LocalDB/Registry.t	2009-01-26 18:04:11.000000000 +0100
> @@ -45,7 +45,7 @@
> 	
> 	SKIP: {
> 		test_skip(-tests => 9,
> -                  -requires_modules => [qw(LWP::UserAgent
> HTTP::Request::Common)],
> +                  -requires_modules => [qw(BerkeleyDB LWP::UserAgent
> HTTP::Request::Common)],
>                   -requires_networking => 1);
> 		
> 		my $registry = Bio::DB::Registry->new();
>
>
>
>
> And a subsequent:
>
> sudo apt-get -y install libberkeleydb-perl && perl t/LocalDB/ 
> Registry.t
>
> ... allowed all 14 tests to pass.
>
> I did not look into why that's the case exactly, but maybe that helps
> you narrow it down.
>
> Chad
>
> On Mon, Jan 26, 2009 at 17:23, Chris Fields <cjfields at illinois.edu>  
> wrote:
>> 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
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l