[mart-dev] ERROR: caught BioMart::Exception::Template __ BioMart web interface error

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[mart-dev] ERROR: caught BioMart::Exception::Template __ BioMart web interface error

Lavigne, Patricia
ERROR: caught BioMart::Exception::Template __ BioMart web interface error

Hi,

I have 1 question about the installation of BioMart.
I follow the instructions http://www.biomart.org/install-overview.html (not for the chapter "Apache and ModPerl quick setup"). When I'm starting MartView, I have the following page. But I don't understand the problem.


#################################### in the browser (Firefox)
ERROR: caught BioMart::Exception::Template: Error in processing template main.tt: plugin error - Number.Format: plugin not found

If you repeatedly get directed to this error page, there may be a problem with your current session parameters. To clear your session and start with a clean slate, please click the New button below.

Stacktrace:
Exception::Class::Base::throw /home/plavigne/src/BioMart/biomart-perl/lib/BioMart/Web.pm:267
BioMart::Web::process_template /home/plavigne/src/BioMart/biomart-perl/lib/BioMart/Web.pm:2577
BioMart::Web::handle_request /home/plavigne/src/BioMart/biomart-perl/cgi-bin/martview:102
(eval) /home/plavigne/src/BioMart/biomart-perl/cgi-bin/martview:101
ModPerl::ROOT::ModPerl::Registry::home_plavigne_src_BioMart_biomart_2dperl_cgi_2dbin_martview::handler /usr/lib/perl5/ModPerl/RegistryCooker.pm:204

(eval) /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run /usr/lib/perl5/ModPerl/RegistryCooker.pm:170
ModPerl::RegistryCooker::default_handler /usr/lib/perl5/ModPerl/Registry.pm:31
ModPerl::Registry::handler -e:0
(eval) -e:0
####################################


I have :
- Ubuntu 9.10 (with VMware Player on Windows XP)
- Apache/2.2.12 (Ubuntu)
- Perl 5, version 12, subversion 1 (v5.12.1) built for i686-linux
- ModPerl 2.0.4 (installed with Synaptic, files mod_perl.so and mod_deflate.so are in /usr/lib/apache2/modules/)
- Number::Format is up to date (1.73).

Below, there is the message on the console for the command (with the response "n") :
perl bin/configure.pl -r conf/registryURLPointer.xml


#################################### in the console
Do you want to install in API only mode [y/n] [n]: 

Checking prerequisites ...[Looks good]

APACHE: /usr/sbin/apache2
HOST: localhost
PORT: 9002
PROXY:
LOCATION: biomart
APXS/2: /usr/bin/apxs2

You can change the above configuration by editing "biomart-perl/conf/settings.conf"



Got usable Apache in /usr/sbin/apache2, probing for version & ModPerl configuration
Have Apache DSO-support and ModPerl library file present, configuring ModPerl in httpd.conf.
Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC
Libdir /home/plavigne/src/BioMart/biomart-perl/lib is not in @INC, adding to @INC

Cached Registry Unavailable...

Running Complete Clean...

Connection parameters of [MSD PROTOTYPE (EBI UK)]       [ OK ]



mkdir /home/plavigne/src/BioMart/biomart-perl/conf/Cached
mkdir /home/plavigne/src/BioMart/biomart-perl/conf/Cached/default
mkdir /home/plavigne/src/BioMart/biomart-perl/conf/Cached/default/confTrees
mkdir /home/plavigne/src/BioMart/biomart-perl/conf/Cached/default/_portables
mkdir /home/plavigne/src/BioMart/biomart-perl/conf/Cached/default/XML

[NEW CONFIGURATION] .... WITH MEMORY [default]
default ... MSD PROTOTYPE (EBI UK) ... 001/001 ... msd ....................................... (WEB) <A HREF="www.biomart.org:80">www.biomart.org:80 ............ ->  upgrading to 0.6/0.7 ... Use of uninitialized value in lc at /home/plavigne/src/BioMart/biomart-perl/bin/../lib/BioMart/Configurator.pm line 460.

Use of uninitialized value in lc at /home/plavigne/src/BioMart/biomart-perl/bin/../lib/BioMart/Configurator.pm line 460.

 OK
Setting possible links between datasets
....(scanning) 100%
....(linking) 100%
....(sorting) 100%
....(clustering) 1/1 - 0 remain    
....(resolving) 100%
Building templates for visible datasets
.... 100%
Compiling templates for visible datasets
[1/1] Attribute Panel of Dataset.. :msd
[1/1] Filter Panel of Dataset..... :msd
####################################


Thank you for your help.
Have a good day.

Patricia.

........................................................................................
Patricia LAVIGNE
Biologiste bioinformaticienne / Biologist bioinformatician


Ressources naturelles Canada, Service canadien des forêts, Centre de foresterie des Laurentides / Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre
1055 rue du P.E.P.S., C.P. 10380 succ. Sainte-Foy, Québec (Québec), Canada G1V 4C7


Téléphone : (418) 648-4947
Télécopieur : (418) 648-5849
........................................................................................


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Re: [mart-dev] ERROR: caught BioMart::Exception::Template __ BioMart web interface error

Syed Haider
Hi Patricia,

please try installing the following perl module:

Template-Plugin-Number-Format

and see if that helps.

Best
Syed

On 03/06/2010 16:51, Lavigne, Patricia wrote:

>
> Hi,
>
> I have 1 question about the installation of BioMart.
> I follow the instructions http://www.biomart.org/install-overview.html (not for the chapter "Apache and ModPerl quick setup"). When I'm starting MartView, I have the following page. But I don't understand the problem.
>
>
> #################################### in the browser (Firefox)
> ERROR: caught BioMart::Exception::Template: Error in processing template main.tt: plugin error - Number.Format: plugin not found
>
> If you repeatedly get directed to this error page, there may be a problem with your current session parameters. To clear your session and start with a clean slate, please click the New button below.
>
> Stacktrace:
> Exception::Class::Base::throw /home/plavigne/src/BioMart/biomart-perl/lib/BioMart/Web.pm:267
> BioMart::Web::process_template /home/plavigne/src/BioMart/biomart-perl/lib/BioMart/Web.pm:2577
> BioMart::Web::handle_request /home/plavigne/src/BioMart/biomart-perl/cgi-bin/martview:102
> (eval) /home/plavigne/src/BioMart/biomart-perl/cgi-bin/martview:101
> ModPerl::ROOT::ModPerl::Registry::home_plavigne_src_BioMart_biomart_2dperl_cgi_2dbin_martview::handler /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
>
> (eval) /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
> ModPerl::RegistryCooker::run /usr/lib/perl5/ModPerl/RegistryCooker.pm:170
> ModPerl::RegistryCooker::default_handler /usr/lib/perl5/ModPerl/Registry.pm:31
> ModPerl::Registry::handler -e:0
> (eval) -e:0
> ####################################
>
>
> I have :
> - Ubuntu 9.10 (with VMware Player on Windows XP)
> - Apache/2.2.12 (Ubuntu)
> - Perl 5, version 12, subversion 1 (v5.12.1) built for i686-linux
> - ModPerl 2.0.4 (installed with Synaptic, files mod_perl.so and mod_deflate.so are in /usr/lib/apache2/modules/)
> - Number::Format is up to date (1.73).
>
> Below, there is the message on the console for the command (with the response "n") :
> perl bin/configure.pl -r conf/registryURLPointer.xml
>
>
> #################################### in the console
> Do you want to install in API only mode [y/n] [n]:
>
> Checking prerequisites ...[Looks good]
>
> APACHE: /usr/sbin/apache2
> HOST: localhost
> PORT: 9002
> PROXY:
> LOCATION: biomart
> APXS/2: /usr/bin/apxs2
>
> You can change the above configuration by editing "biomart-perl/conf/settings.conf"
>
>
>
> Got usable Apache in /usr/sbin/apache2, probing for version&  ModPerl configuration
> Have Apache DSO-support and ModPerl library file present, configuring ModPerl in httpd.conf.
> Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC
> Libdir /home/plavigne/src/BioMart/biomart-perl/lib is not in @INC, adding to @INC
>
> Cached Registry Unavailable...
>
> Running Complete Clean...
>
> Connection parameters of [MSD PROTOTYPE (EBI UK)]       [ OK ]
>
>
>
> mkdir /home/plavigne/src/BioMart/biomart-perl/conf/Cached
> mkdir /home/plavigne/src/BioMart/biomart-perl/conf/Cached/default
> mkdir /home/plavigne/src/BioMart/biomart-perl/conf/Cached/default/confTrees
> mkdir /home/plavigne/src/BioMart/biomart-perl/conf/Cached/default/_portables
> mkdir /home/plavigne/src/BioMart/biomart-perl/conf/Cached/default/XML
>
> [NEW CONFIGURATION] .... WITH MEMORY [default]
> default ... MSD PROTOTYPE (EBI UK) ... 001/001 ... msd ....................................... (WEB) www.biomart.org:80 ............ ->   upgrading to 0.6/0.7 ... Use of uninitialized value in lc at /home/plavigne/src/BioMart/biomart-perl/bin/../lib/BioMart/Configurator.pm line 460.
>
> Use of uninitialized value in lc at /home/plavigne/src/BioMart/biomart-perl/bin/../lib/BioMart/Configurator.pm line 460.
>
>   OK
> Setting possible links between datasets
> ....(scanning) 100%
> ....(linking) 100%
> ....(sorting) 100%
> ....(clustering) 1/1 - 0 remain
> ....(resolving) 100%
> Building templates for visible datasets
> .... 100%
> Compiling templates for visible datasets
> [1/1] Attribute Panel of Dataset.. :msd
> [1/1] Filter Panel of Dataset..... :msd
> ####################################
>
>
> Thank you for your help.
> Have a good day.
>
> Patricia.
>
> ........................................................................................
> Patricia LAVIGNE
> Biologiste bioinformaticienne / Biologist bioinformatician
>
> Ressources naturelles Canada, Service canadien des forêts, Centre de foresterie des Laurentides / Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre
> 1055 rue du P.E.P.S., C.P. 10380 succ. Sainte-Foy, Québec (Québec), Canada G1V 4C7
>
> Téléphone : (418) 648-4947
> Télécopieur : (418) 648-5849
> ........................................................................................
>
>
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RE: [mart-dev] ERROR: caught BioMart::Exception::Template __ BioMart web interface error

Lavigne, Patricia
Hi Syed,

I already have this module.
- Template::Plugin::Number::Format is up to date (1.02).


Thanks.
Patricia.
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Re: [mart-dev] ERROR: caught BioMart::Exception::Template __ BioMart web interface error

Syed Haider
Please send me the logs/error_logs file. The email list would reject any
attachments.

Best
Syed



On 03/06/2010 17:24, Lavigne, Patricia wrote:
> Hi Syed,
>
> I already have this module.
> - Template::Plugin::Number::Format is up to date (1.02).
>
>
> Thanks.
> Patricia.
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RE: ERROR: caught BioMart::Exception::Template __ BioMart web interface error

Lavigne, Patricia
Hi,

Resolved problem. Thanks Syed.

See the following page (given by Syed):
https://bugs.launchpad.net/ubuntu/+source/libsvn-web-perl/+bug/269542


I already have (see Synaptic):
- libtimedate-perl 1.1600-9
- libnumber-format-perl 1.70-1

After :
- I created the directory /usr/share/perl5/Template/Plugin/Number/ (root).
- I downloaded the file Template-Plugin-Number-Format-1.02.tar.gz (from http://search.cpan.org/~darren/Template-Plugin-Number-Format-1.02/Format.pm) and unpacked it.
- And I copied the file Format.pm in the directory :

sudo cp  /home/plavigne/.cpan/sources/modules/Template-Plugin-Number-Format-1.02/Format.pm   /usr/share/perl5/Template/Plugin/Number/


Thanks.
Patricia.



-----Message d'origine-----
De : Syed Haider
Envoyé : juin 3, 2010 13:25
À : Lavigne, Patricia
Objet : Re: [mart-dev] ERROR: caught BioMart::Exception::Template __ BioMart web interface error

Hi Patricia,

here is the answer to your question:

https://bugs.launchpad.net/ubuntu/+source/libsvn-web-perl/+bug/269542

the problem seems to be with the perl module i referred earlier on.

Let me if that helps.

Best
Syed

On 03/06/2010 18:09, Lavigne, Patricia wrote:
> Hi,
>
> My files.
>
> Thanks.
> Patricia.
>
>
>