[ensembl-dev] changed code causes errr

[Andy Yates]

Hi there,

As Jay said installing HTML::Strip is the right thing to do here. However your error reports seem to suggest something else is going wrong here

1). Your website's @INC contains references to Perl 5.10.1

2). Your CPAN path contains a reference to Perl 5.14.1. That's in conflict with 5.10.1 & *will* cause issues as HTML::Strip uses C 

3). Pushing an unshift into @INC in WebsiteAdaptor seems like a massive hack & the wrong place to put the library location in. I always thought this kind of thing should go into SiteDefs and push into @SiteDefs::ENSEMBL_PERL_DIRS but this is something I'd delegate onto the webteam to make a call about

To remedy this I would attempt an installation of HTML::Strip into the Perl 5.10.1 library path. If this is a system provided version of Perl i.e. what your linux/os installation shipped with then use the OS's package management software to install the dependency.

Hope some of this has helped,

Andy

Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 18 May 2012, at 08:49, 陈岗 wrote:

> Hi All
> 
> I updated Ensembl from release-66 to 67, and get following error message:
> 
> 
> !!! UNKNOWN RSS METHOD DEFINED at /usr/local/Ensembl/modules/EnsEMBL/Web/Document/HTML.pm line 143.
> EnsEMBL::Web::Root: failed to use EnsEMBL::Web::Document::HTML::WhatsNew
> EnsEMBL::Web::Root: Can't locate HTML/Strip.pm in @INC (@INC contains: /usr/local/Ensembl/public-plugins/ensembl/modules /usr/local/Ensembl/public-plugins/ensembl/modules /usr/local/Ensembl/ensembl/modules /usr/local/Ensembl/ensembl-compara/modules /usr/local/Ensembl/ensembl-draw/modules /usr/local/Ensembl/ensembl-variation/modules /usr/local/Ensembl/ensembl-functgenomics/modules /usr/local/Ensembl/ensembl-external/modules /usr/local/Ensembl/bioperl-live /usr/local/Ensembl/modules /usr/local/Ensembl/conf/ /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl . /usr/local/Ensembl) at /usr/local/Ensembl/modules/EnsEMBL/Web/DBSQL/WebsiteAdaptor.pm line 12.
> BEGIN failed--compilation aborted at /usr/local/Ensembl/modules/EnsEMBL/Web/DBSQL/WebsiteAdaptor.pm line 12.
> Compilation failed in require at /usr/local/Ensembl/modules/EnsEMBL/Web/Document/HTML/WhatsNew.pm line 11.
> BEGIN failed--compilation aborted at /usr/local/Ensembl/modules/EnsEMBL/Web/Document/HTML/WhatsNew.pm line 11.
> Compilation failed in require at (eval 325) line 3.
>  at /usr/local/Ensembl/modules/EnsEMBL/Web/Root.pm line 136
>         EnsEMBL::Web::Root::dynamic_use('EnsEMBL::Web::Controller::SSI=HASH(0x6a30ee8)', 'EnsEMBL::Web::Document::HTML::WhatsNew') called at /usr/local/Ensembl/modules/EnsEMBL/Web/Controller.pm line 395
>         EnsEMBL::Web::Controller::_use('EnsEMBL::Web::Controller::SSI=HASH(0x6a30ee8)', 'EnsEMBL::Web::Document::HTML::WhatsNew', 'EnsEMBL::Web::Hub=HASH(0x6937990)') called at /usr/local/Ensembl/modules/EnsEMBL/Web/Controller/SSI.pm line 167
>         EnsEMBL::Web::Controller::SSI::template_SCRIPT('EnsEMBL::Web::Controller::SSI=HASH(0x6a30ee8)', undef) called at /usr/local/Ensembl/modules/EnsEMBL/Web/Controller/SSI.pm line 78
>         EnsEMBL::Web::Controller::SSI::content('EnsEMBL::Web::Controller::SSI=HASH(0x6a30ee8)') called at /usr/local/Ensembl/modules/EnsEMBL/Web/Controller/SSI.pm line 87
>         EnsEMBL::Web::Controller::SSI::render_page('EnsEMBL::Web::Controller::SSI=HASH(0x6a30ee8)') called at /usr/local/Ensembl/modules/EnsEMBL/Web/Controller/SSI.pm line 47
>         EnsEMBL::Web::Controller::SSI::_init('EnsEMBL::Web::Controller::SSI=HASH(0x6a30ee8)') called at /usr/local/Ensembl/modules/EnsEMBL/Web/Controller/SSI.pm line 22
>         EnsEMBL::Web::Controller::SSI::init('EnsEMBL::Web::Controller::SSI=HASH(0x6a30ee8)') called at /usr/local/Ensembl/modules/EnsEMBL/Web/Controller.pm line 91
>         EnsEMBL::Web::Controller::new('EnsEMBL::Web::Controller::SSI', 'Apache2::RequestRec=SCALAR(0x255f5f0)', 'HASH(0x68ff648)') called at /usr/local/Ensembl/modules/EnsEMBL/Web/Apache/SSI.pm line 64
>         EnsEMBL::Web::Apache::SSI::handler('Apache2::RequestRec=SCALAR(0x255f5f0)', 'HASH(0x68ff648)') called at /usr/local/Ensembl/modules/EnsEMBL/Web/Apache/Handlers.pm line 473
>         EnsEMBL::Web::Apache::Handlers::handler('Apache2::RequestRec=SCALAR(0x255f5f0)') called at -e line 0
>         eval {...} called at -e line 0
> [Fri May 18 14:13:13 2012] [error] [client 192.168.30.5] Can't locate object method "render" via package "EnsEMBL::Web::Document::HTML::WhatsNew" at /usr/local/Ensembl/modules/EnsEMBL/Web/Controller/SSI.pm line 174.\n
> 
> 
> I installed package HTML::Strip from CPAN, add its directory to WebsiteAdaptor.pm, as
> 
> BEGIN {unshift (@INC,'/usr/local/lib/perl5/site_perl/5.14.1/x86_64-linux-thread-multi'); }
> 
> But still get error: 
> 
> !!! UNKNOWN RSS METHOD DEFINED at /usr/local/Ensembl/modules/EnsEMBL/Web/Document/HTML.pm line 143.
> EnsEMBL::Web::Root: failed to use EnsEMBL::Web::Document::HTML::WhatsNew
> EnsEMBL::Web::Root: Can't locate HTML/Strip.pm in @INC (@INC .........................
> ...........................................................................................................................
> 
> Where should I modify the directory  ?
> 
> Thanks
> -- 
> Gang Chen
> TILSI
> Taicang Institute For Life Science Information
> Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province, P.R.China
> Phone:（+86）512-82782588
> 
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