[Bioperl-l] [Bioperl-guts-l] Notification: incoming/1277 (fwd)

[Hilmar Lapp]

I've sent this multiple times already. If anyone is willing to help 
put up an FAQ or help ChrisD update his guide, that'd be great, I 
just don't have much time right now. Clearly the README needs 
revision, but I have to fix and write certain pieces of bioperl-db 
code first.

Again for the records: across the board the branches 
bioperl-release-1-1-0 are considered production as far as bioperl-db 
is concerned. I.e., you need to download that branch tag from 
biosql-schema and bioperl-db. This branch on bioperl-live is 
equivalent to the 1.1.0 development release to be found on the 
bioperl.org server (not an CPAN; does anyone have the URL handy?).

The alternative is to use the main trunk versions across the board 
(yes, all three need to be main trunk then). I'd only recommend that 
if you know and like living on the bleeding edge, as you will have 
to update the checkouts from cvs regularly and re-install regularly 
to incorporate fixes etc. It's not difficult to do, but it can be 
intimidating if you're not used to it.

	-hilmar

On Monday, October 28, 2002, at 06:40 AM, Jason Stajich wrote:

> You can't use bioperl 1.0.X with the latest bioperl-db code - you 
> need to
> checkout the freeze versions which I can't remember off the top of 
> my head
> which version is the correct one.  Hilmar/Chris - would it be 
> possible for
> you or someone to write a simple list of dependancies and throw it 
> up on
> the OBDA webpage so we can refer people to it?
>
> Thanks.
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
> ---------- Forwarded message ----------
> Date: Mon, 28 Oct 2002 07:48:05 -0500
> From: bioperl-bugs@bioperl.org
> To: bioperl-guts-l@bioperl.org
> Subject: [Bioperl-guts-l] Notification: incoming/1277
>
> JitterBug notification
>
> new message incoming/1277
>
> Message summary for PR#1277
> 	From: Guido Dieterich <Guido.Dieterich@gbf.de>
> 	Subject: when I try to run  ....
> 	Date: Mon, 28 Oct 2002 14:55:37  0100
> 	0 replies 	0 followups
>
> ====> ORIGINAL MESSAGE FOLLOWS <====
>
>> From Guido.Dieterich@gbf.de  Mon Oct 28 07:48:04 2002
> Return-Path: <Guido.Dieterich@gbf.de>
> Received: from gg.gbf.de (gg.gbf.de [193.175.244.3])
> 	by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g9SCm36J004293
> 	for <bioperl-bugs@bio.perl.org>; Mon, 28 Oct 2002 07:48:04 -0500
> Received: by gg.gbf.de (8.11.6/8.11.6) id g9SDtiM19572
> 	for bioperl-bugs@bio.perl.org; Mon, 28 Oct 2002 14:55:44 +0100 (CET)
> Received: (from localhost) by rzgate.gbf.de (MSCAN) id 
> 3/rzgate.gbf.de/smtp-gw/mscan; Mon Oct 28 14:55:44 2002
> Message-ID: <3DBD41D9.2010107@gbf.de>
> Date: Mon, 28 Oct 2002 14:55:37 +0100
> From: Guido Dieterich <Guido.Dieterich@gbf.de>
> User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2b) 
> Gecko/20021016
> X-Accept-Language: en-us, en
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> To: bioperl-bugs@bio.perl.org
> Subject: when I try to run  ....
> Content-Type: text/plain; charset=us-ascii; format=flowed
> Content-Transfer-Encoding: 7bit
> X-AntiVirus: checked by AntiVir MailGate (version: 2.0.1.6; AVE: 
> 6.16.0.0; VDF: 6.16.0.9; host: rzlimes)
>
> perl ./load_seqdatabase.pl
>
> -------------------- WARNING ---------------------
> MSG: failed to load dbadaptor: Can't locate object method 
> "_load_module"
> via package "Bio::DB::BioDB" (perhaps you forgot to load
> "Bio::DB::BioDB"?) at /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioDB.pm
> line 153.
>
> Can't locate object method "_load_module" via package "Bio::DB::BioDB"
> (perhaps you forgot to load "Bio::DB::BioDB"?) at
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioDB.pm line 153.
>
> ---------------------------------------------------
>
> ------------- EXCEPTION  -------------
> MSG: fatal: unable to load DBAdaptor for database:
> Bio::DB::BioSQL::{DBAdaptor,dbadaptor} all failed to load
> STACK Bio::DB::BioDB::new 
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioDB.pm:120
> STACK toplevel ./load_seqdatabase.pl:130
>
> --------------------------------------
> suse8.0
>
>
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--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------