[ensembl-dev] Warnings when running VEP INSTALL script
Andy Yates
ayates at ebi.ac.uk
Tue Jan 22 21:05:16 GMT 2013
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
>
>
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