[Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0

[Chad Davis]

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
>>>
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>