[Bioperl-l] Fwd: Re: Bio::DB::BioDB

[Hilmar Lapp]

Madhuri,

please do NOT send personal email to Heikki or any other developer with 
questions or reports concerning any software module. Otherwise you risk 
that your emails remain unanswered. There's many people on the mailing 
list who can possibly help you out.

As for your report, I fixed the cause for this in bioperl-db. You need 
to update from cvs, or download the tarball and re-install. The change 
is in a single file, namely Bio/DB/Persistent/PersistentObject.pm. The 
new version should have the revision line
$Id: PersistentObject.pm,v 1.5 2005/06/26 17:38:22 lapp Exp $
at the top of the file.

	-hilmar

On Jun 25, 2005, at 2:41 AM, lehvasla at ebi.ac.uk wrote:

>
> From: madhuri battu <madhuri_battu at yahoo.co.in>
> Date: June 24, 2005 4:33:46 PM EDT
> To: Heikki Lehväslaiho <heikki at ebi.ac.uk>
> Subject: Re: Bio::DB::BioDB
>
>
> Hi,
>   I loaded the whole Bioperl through cvs and i tried
> to run load_seqdatabase.pl script on my machine and i
> am getting the following errors
>
> Could not store NM_000014: Operation `ne': no method
> found,
>         left argument in overloaded package
> Bio::Annotation::Reference,
>         right argument has no overloaded magic at
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm
> line534, <GEN0> line 581.
>
> Can you please help me in this matter.
> Thanks,
> Madhuri.
> --- Heikki Lehvaslaiho <heikki at ebi.ac.uk> wrote:
>
>> Madhuri,
>>
>> It should work from CVS. I've forwarded your message
>> to the bioperl mailing
>> list (bioperl-l at bioperl.org). Please further queries
>> and more detailed
>> problem reports there.
>>
>> If you have downloaded bioperl-db from CVS, you need
>> to add its root directory
>> to your PERL5LIB environmental variable.
>>
>>
> PERL5LIB=/home/heikki/src/bioperl/core:/home/heikki/src/bioperl/db
>>
>> More generic bioperl install instructions can be
>> found at:
>>
> http://www.ebi.ac.uk/~lehvasla/bioperl/InstallingBioperl.html
>>
>>
>>  -Heikki
>>
>> On Thursday 23 June 2005 19:47, madhuri battu wrote:
>>> Hi,
>>>   My name is Madhuri Battu. I am working at UT
>>> Southwestern in US as an intern. I have a problem
>> with
>>> installing Bio::DB::BioDB. It was saying it is 5
>> years
>>> old on downloads page and recently updated on View
>> cvs
>>> page. Can you please tell whether the module is
>> being
>>> used and how can i install it. If this module is
>> not
>>> being used what module can be used in place of
>> that.
>>> Thanks,
>>> Madhuri.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
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>> -- 
>> ______ _/
>>
> _/_____________________________________________________
>>       _/      _/
>> http://www.ebi.ac.uk/mutations/
>>      _/  _/  _/  Heikki Lehvaslaiho    heikki at_ebi
>> _ac _uk
>>     _/_/_/_/_/  EMBL Outstation, European
>> Bioinformatics Institute
>>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>>   _/  _/  _/  Cambridge, CB10 1SD, United Kingdom
>>      _/      Phone: +44 (0)1223 494 644   FAX: +44
>> (0)1223 494 468
>> ___
>>
> _/_/_/_/_/________________________________________________________
>>
>
>
>
> 		
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------