[BioMart Users] BioMart 0.8 rc4 (icgc users)

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[BioMart Users] BioMart 0.8 rc4 (icgc users)

Syed Haider
Hello Everyone,

We have noticed few problems with icgc3.xml in the latest release
(release candidate 4). We are in the process of fixing these and should
update you as soon as the patch is propagated to the rc4 branch.

Meanwhile we apologise for any inconvenience this may have caused.

Best,
Syed Haider
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Re: [BioMart Users] BioMart 0.8 rc4 (icgc users)

Jorge Zamora Berna
Hi Syed,

does it mean that the file icgc3.xml in rc3 is different to the one that comes with rc4? I just say that since I have used the same copy of the xml  file in both release candidates but it's only under RC4 when I experience problems?

Might be something else apart from the xml file itself?

Thanks,
Jorge


--- El jue, 3/2/11, Syed Haider <[hidden email]> escribió:

> De: Syed Haider <[hidden email]>
> Asunto: [BioMart Users] BioMart 0.8 rc4 (icgc users)
> Para: "[hidden email]" <[hidden email]>
> Fecha: jueves, 3 de febrero, 2011 18:36
> Hello Everyone,
>
> We have noticed few problems with icgc3.xml in the latest
> release (release candidate 4). We are in the process of
> fixing these and should update you as soon as the patch is
> propagated to the rc4 branch.
>
> Meanwhile we apologise for any inconvenience this may have
> caused.
>
> Best,
> Syed Haider
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
>


     
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Re: [BioMart Users] BioMart 0.8 rc4 (icgc users)

Jorge Zamora Berna
Hi again Syed,

Just to better explain what is happening to me with rc4 (as ICGC user) is that I don't get back simple mutations under the 'QUICK' interface. I get simple mutations when using the other two interfaces but with a limited number of selected attributes (that is not all of them).

Hope this helps,
Jorge.



--- El vie, 4/2/11, Jorge Zamora Berna <[hidden email]> escribió:

> De: Jorge Zamora Berna <[hidden email]>
> Asunto: Re: [BioMart Users] BioMart 0.8 rc4 (icgc users)
> Para: "[hidden email]" <[hidden email]>, "Syed Haider" <[hidden email]>
> Fecha: viernes, 4 de febrero, 2011 09:00
> Hi Syed,
>
> does it mean that the file icgc3.xml in rc3 is different to
> the one that comes with rc4? I just say that since I have
> used the same copy of the xml  file in both release
> candidates but it's only under RC4 when I experience
> problems?
>
> Might be something else apart from the xml file itself?
>
> Thanks,
> Jorge
>
>
> --- El jue, 3/2/11, Syed Haider <[hidden email]>
> escribió:
>
> > De: Syed Haider <[hidden email]>
> > Asunto: [BioMart Users] BioMart 0.8 rc4 (icgc users)
> > Para: "[hidden email]"
> <[hidden email]>
> > Fecha: jueves, 3 de febrero, 2011 18:36
> > Hello Everyone,
> >
> > We have noticed few problems with icgc3.xml in the
> latest
> > release (release candidate 4). We are in the process
> of
> > fixing these and should update you as soon as the
> patch is
> > propagated to the rc4 branch.
> >
> > Meanwhile we apologise for any inconvenience this may
> have
> > caused.
> >
> > Best,
> > Syed Haider
> > _______________________________________________
> > Users mailing list
> > [hidden email]
> > https://lists.biomart.org/mailman/listinfo/users
> >
>
>
>      
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
>


     
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Re: [BioMart Users] BioMart 0.8 rc4 (icgc users)

Syed Haider
Hi Jorge,

we are aware of this problem and in the process of fixing this. The
icgc3.xml for rc4 should be identical to rc3 for the end-user except few
internal changes that should not have any impact on icgc users. The one
with rc4 happened to have some problems and we are preparing a patch for
this right now. We will update you as soon as (hopefully today) this is
fixed.

Thanks for your patience,
Syed

On 04/02/2011 08:21, Jorge Zamora Berna wrote:

> Hi again Syed,
>
> Just to better explain what is happening to me with rc4 (as ICGC user) is that I don't get back simple mutations under the 'QUICK' interface. I get simple mutations when using the other two interfaces but with a limited number of selected attributes (that is not all of them).
>
> Hope this helps,
> Jorge.
>
>
>
> --- El vie, 4/2/11, Jorge Zamora Berna<[hidden email]>  escribió:
>
>> De: Jorge Zamora Berna<[hidden email]>
>> Asunto: Re: [BioMart Users] BioMart 0.8 rc4 (icgc users)
>> Para: "[hidden email]"<[hidden email]>, "Syed Haider"<[hidden email]>
>> Fecha: viernes, 4 de febrero, 2011 09:00
>> Hi Syed,
>>
>> does it mean that the file icgc3.xml in rc3 is different to
>> the one that comes with rc4? I just say that since I have
>> used the same copy of the xml  file in both release
>> candidates but it's only under RC4 when I experience
>> problems?
>>
>> Might be something else apart from the xml file itself?
>>
>> Thanks,
>> Jorge
>>
>>
>> --- El jue, 3/2/11, Syed Haider<[hidden email]>
>> escribió:
>>
>>> De: Syed Haider<[hidden email]>
>>> Asunto: [BioMart Users] BioMart 0.8 rc4 (icgc users)
>>> Para: "[hidden email]"
>> <[hidden email]>
>>> Fecha: jueves, 3 de febrero, 2011 18:36
>>> Hello Everyone,
>>>
>>> We have noticed few problems with icgc3.xml in the
>> latest
>>> release (release candidate 4). We are in the process
>> of
>>> fixing these and should update you as soon as the
>> patch is
>>> propagated to the rc4 branch.
>>>
>>> Meanwhile we apologise for any inconvenience this may
>> have
>>> caused.
>>>
>>> Best,
>>> Syed Haider
>>> _______________________________________________
>>> Users mailing list
>>> [hidden email]
>>> https://lists.biomart.org/mailman/listinfo/users
>>>
>>
>>
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>>
>
>
>
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[BioMart Users] BioMart 0.8 rc4 (icgc3 patch)

Syed Haider
In reply to this post by Syed Haider
Dear All,

The icgc3.xml specific problems are now fixed, please run `svn update`
followed by `ant` to get the patch working.

Thanks very much for your patience,
Syed Haider


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