Render bug

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

Render bug

nhani_cnpt
Hi,

I'm reconfiguring GBrowse 2.03 after a failled attept to upgrade to  
2.13, and the following message popped-up:

--
gbrowse: BUG: working around no ref defined bug; tell Lincoln bug is  
not fixed at /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/Bio/
Graphics/Browser2/Render.pm line 2463., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
--

I've never seen this message before...

Cheers,

Antonio


Antonio Nhani Jr
Núcleo de Melhoramento e Biotecnologia
54 3316 5833 / 5829
Embrapa Trigo - Rod. BR 285 Km 294
99001-970 Passo Fundo/RS



------------------------------
Aviso de confidencialidade:

- Esta mensagem da Empresa Brasileira de Pesquisa Agropecuária (Embrapa), empresa pública federal regida pelo disposto na Lei Federal nº 5.851, de 7 de dezembro de 1972, é enviada exclusivamente a seu destinatário e pode conter informações confidenciais, protegidas por sigilo profissional. Sua utilização desautorizada é ilegal e sujeita o infrator às penas da lei. Se você a recebeu indevidamente, queira, por gentileza, reenviá-la ao emitente, esclarecendo o equívoco.

Confidentiality note:

- "This message from Empresa Brasileira de Pesquisa Agropecuária (Embrapa), a government company established under Brazilian law (5.851/72), is directed exclusively to its addressee and may contain confidential data, protected under professional secrecy rules. Its unauthorized use is illegal and may subject the transgressor to the law's penalties. If you are not the addressee, please send it back, elucidating the failure".

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: Render bug

Scott Cain
Hi Antonio,

I think that bug has been addressed.  We're up to version 2.15 for
GBrowse, so I suggest you try moving to that, but make sure that you
also get current versions of Bio::Graphics and Bio::DB::Das::Chado.

Scott


On Tue, Sep 14, 2010 at 7:25 PM, nhani_cnpt <[hidden email]> wrote:

> Hi,
>
> I'm reconfiguring GBrowse 2.03 after a failled attept to upgrade to
> 2.13, and the following message popped-up:
>
> --
> gbrowse: BUG: working around no ref defined bug; tell Lincoln bug is
> not fixed at /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/Bio/
> Graphics/Browser2/Render.pm line 2463., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast/
> --
>
> I've never seen this message before...
>
> Cheers,
>
> Antonio
>
>
> Antonio Nhani Jr
> Núcleo de Melhoramento e Biotecnologia
> 54 3316 5833 / 5829
> Embrapa Trigo - Rod. BR 285 Km 294
> 99001-970 Passo Fundo/RS
>
>
>
> ------------------------------
> Aviso de confidencialidade:
>
> - Esta mensagem da Empresa Brasileira de Pesquisa Agropecuária (Embrapa), empresa pública federal regida pelo disposto na Lei Federal nº 5.851, de 7 de dezembro de 1972, é enviada exclusivamente a seu destinatário e pode conter informações confidenciais, protegidas por sigilo profissional. Sua utilização desautorizada é ilegal e sujeita o infrator às penas da lei. Se você a recebeu indevidamente, queira, por gentileza, reenviá-la ao emitente, esclarecendo o equívoco.
>
> Confidentiality note:
>
> - "This message from Empresa Brasileira de Pesquisa Agropecuária (Embrapa), a government company established under Brazilian law (5.851/72), is directed exclusively to its addressee and may contain confidential data, protected under professional secrecy rules. Its unauthorized use is illegal and may subject the transgressor to the law's penalties. If you are not the addressee, please send it back, elucidating the failure".
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Loading chado XML

Richard Smith
Hi all,
We're looking for some advice on loading chado XML files into chado
databases in the modENCODE project.

We're loading hundreds of chado XML files into a single chado
database, files vary in size but some are 1-2GB.  We're using
stag-storenode.pl to do this and are running into problems with the
large files.

http://search.cpan.org/~scain/DBIx-DBStag-0.12/scripts/stag-storenode.pl

For files that are 1-2GB in size containing hundreds of thousands of
features this takes 8-12 hours per file.  Our process is such that we
usually load files incrementally (which is slow) but sometimes have to
re-build the chado database from all the source chado XML files, which
takes around two weeks.

Does anyone load similar sized files more quickly?  Perhaps there are
alternatives to stag-storenode?  If anyone can offer advice or describe
their experiences I would be very grateful.

Cheers,
Richard.

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema