[ensembl-dev] [Ensembl-variation] Bio::EnsEMBL::Variation::TranscriptVariationAllele

[Sung Gong]

Hi Sarah,

I could not see any problem after a fresh install:
cvs -d :pserver:cvsuser at cvs.sanger.ac.uk:/cvsroot/ensembl checkout -r
branch-ensembl-69 ensembl-variation

Previously, I tried to update existing local ensembl via:
cvs -q update -d -P -r branch-ensembl-69

Do I have to do a fresh install rather than an update?
Can you review the document below regarding CVS update?
http://www.ensembl.org/info/docs/api/api_cvs.html

Cheers,
Sung

On 21 November 2012 14:13, Sarah Hunt <seh at ebi.ac.uk> wrote:

> Hi Sung,
>
> Did you pick up the new API version by CVS checkout? If so, can you
> try checking out a new version to a different location and see if you
> still have this problem.
>
> Also - there is no need to send queries to the variation team as well
> as dev at ensembl.org. We all receive the messages to dev at ensembl.org, so
> this is the only address you need use.
>
> Best wishes,
>
> Sarah
>
> On Wed, Nov 21, 2012 at 1:30 PM, Sung Gong <sung at bio.cc> wrote:
> > This one as well:
> > Exception syntax error at
> >
> ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> > line 777, near "elsif"
> >
> >
> > On 21 November 2012 13:25, Sung Gong <sung at bio.cc> wrote:
> >>
> >> Hi,
> >>
> >> In 69 API version, I found followings:
> >>
> >> Use of bare << to mean <<"" is deprecated at
> >>
> ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> >> line 767.
> >> Use of bare << to mean <<"" is deprecated at
> >>
> ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> >> line 776.
> >>
> >> Can you debug this and update CVS please?
> >>
> >> Cheers,
> >> Sung
> >>
> >>
> >> On 22 August 2012 14:33, Sarah Hunt <seh at ebi.ac.uk> wrote:
> >>>
> >>> Hi Sung,
> >>>
> >>> Thanks for reporting this one. It has been updated in CVS now.
> >>>
> >>> Best wishes,
> >>>
> >>> Sarah
> >>>
> >>> On Wed, Aug 22, 2012 at 2:15 PM, Sung Gong <sung at bio.cc> wrote:
> >>> > Hi,
> >>> >
> >>> > In 68 API version, you may have forgotten to write a debug flag?
> >>> >
> >>> > at line 742
> >>> > print "formating a dup  $hgvs_notation->{hgvs} \n" if $DEBUG==1;
> >>> > rather than
> >>> > print "formating a dup  $hgvs_notation->{hgvs} \n";
> >>> >
> >>> > Can you update CVS please?
> >>> >
> >>> > Cheers,
> >>> > Sung
> >>> > _______________________________________________
> >>
> >>
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20121121/a2388767/attachment.html>