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

[Sarah Hunt]

Hi Sung,

It's good to hear this fixes the problem.

As you are no doubt aware, CVS flags potential conflicts between
non-checked in edits in your local version and the version you are
updating to with '<<<<<<<' and  '>>>>>>>'  and I suspect this caused
the problem you saw.

The documentation you refer to assumes the CVS checkout has not been
modified locally. If you have made modifications and are interested in
keeping them you would need to check and resolve any conflicts,
otherwise it is easier to do a fresh install.

Best wishes,

Sarah

On Wed, Nov 21, 2012 at 2:49 PM, Sung Gong <sung at bio.cc> wrote:
> 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
>> >>> > _______________________________________________
>> >>
>> >>
>> >
>
>