[Bioc-devel] github mirror out of sync for ensembldb

[Leonardo Collado Torres]

Hi,

Ahh, ok. What I meant was that the "master" branch in
Bioconductor-mirror is not up to date with bioc-devel. I could see
that aCGH did have a release-3.5 branch, but that the "master" branch
wasn't updated. You can see something similar for
https://github.com/Bioconductor-mirror/derfinder/branches where
https://github.com/Bioconductor-mirror/derfinder/blob/master/DESCRIPTION#L5
shows version 1.9.11 while bioc-devel's
http://bioconductor.org/packages/devel/bioc/html/derfinder.html is at
1.11.0

Basically, the equivalent of older commits like
https://github.com/Bioconductor-mirror/derfinder/commit/4687d52b8c6fda6541d2454bda1517ed2776d351
and https://github.com/Bioconductor-mirror/derfinder/commit/a0f94bae0270f390afc00468d953237f44722790
are missing.

Best,
Leo

On Wed, May 3, 2017 at 1:54 PM, Rainer Johannes
<Johannes.Rainer at eurac.edu> wrote:
>
>
>> On 3 May 2017, at 19:51, Martin Morgan <Martin.Morgan at RoswellPark.org> wrote:
>>
>> On 05/03/2017 01:10 PM, Leonardo Collado Torres wrote:
>>> Hi,
>>>
>>> I don't think that any of the Bioconductor-mirror repos have been
>>> updated to match the current bioc-devel branch. For example, look at
>>> https://github.com/Bioconductor-mirror/aCGH/blob/master/DESCRIPTION#L4
>>> which is one of the first packages by alphabetical order. My guess is
>>> that they are working on the svn to git transition plan described at
>>> https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010691.html.
>>
>> That's not correct, the repositories should be (in general) up to date. I believe Johannes' package is current (sorry, by the time I got to it it had healed itself and I didn't respond to the list).
>>
>
> No prob. I've made an update to the package and after committing the change to the Bioc svn ensembldb was synced successfully.
>
>> aCGH actually had a RELEASE_3_5 branch; I'll investigate why aCGH and at least some other packages have not been fully updated after the branch.
>>
>> Martin
>>
>>
>>>
>>> Best,
>>> Leo
>>>
>>> On Thu, Apr 27, 2017 at 6:52 AM, Rainer Johannes
>>> <Johannes.Rainer at eurac.edu> wrote:
>>>> Hi,
>>>>
>>>> the github mirror for ensembldb seems to be out of sync with the BioC svn, i.e. the DESCRIPTION in https://github.com/Bioconductor-mirror/ensembldb/blob/master/DESCRIPTION is still at version 1.99.14 while in the svn it's already 2.1.0.
>>>>
>>>> First I thought the sync is not yet finished, but the release-3.5 was already created on the github mirror, so I guess sync must have been stuck somewhere.
>>>>
>>>>
>>>>
>>>>
>>>>        [[alternative HTML version deleted]]
>>>>
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>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
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>>>
>>
>>
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