[ensembl-dev] Warnings when running VEP INSTALL script

[Aaron Day-Williams]

Hi Andy,

Thanks for the tip.  That fixed the warnings.

Cheers,

Aaron

-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Andy Yates
Sent: Tuesday, January 22, 2013 4:05 PM
To: Ensembl developers list
Cc: dev at ensembl.org
Subject: Re: [ensembl-dev] Warnings when running VEP INSTALL script

Hi Aaron

This kind of error can be caused by a merge conflict if you've updated using cvs. I would recommend deleting your module

> ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm

And then request an update from the server. Cvs should recognise the missing file and will pull a fresh copy from the repository. 

Hope this helps

Andy

Sent from my mobile.

On 22 Jan 2013, at 20:29, Aaron Day-Williams <Aaron.Day-Williams at biogenidec.com> wrote:

> Hi,
> 
> I've updated my API installations to release 70 and downloaded and am installing the VEP v2.8.  When I run the INSTALL.pl script in the VEP tarball I get the following warnings:
> 
> 
> Checking for installed versions of the Ensembl API...
> Use of bare << to mean <<"" is deprecated at /ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 48.
> Use of bare << to mean <<"" is deprecated at /ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 56.
> Argument "use Bio::EnsEMBL::Registry;\nuse Bio::EnsEMBL::Variation..." isn't numeric in left bitshift (<<) at /ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 67.
> Argument "use File::Path;# qw(make_path);\n=======\nuse File::Path..." isn't numeric in left bitshift (<<) at /ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 67.
> Done
> 
> Is this something on my end or something in the VEP.pm module that needs to be fixed?
> 
> Thanks,
> 
> Aaron
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

_______________________________________________
Dev mailing list    Dev at ensembl.org
Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
Ensembl Blog: http://www.ensembl.info/