[Bioc-devel] [SPAM???] Re: Pushing updates in the release branch

Charles Joly charles.joly-beauparlant at crchul.ulaval.ca
Fri May 27 14:43:46 CEST 2016

Hello Valerie,

The tricky part with Encode is that there is no release schedule. For
instance, in the last month, there has been a few hundreds new datasets (
https://www.encodeproject.org/news/). I think there is an increase in the
amount of data submitted before the Encode users meeting in june.

To update the `encode_df`, it takes ~15 minutes just to query the REST API
to download all the tables used to produce it. There is a search in the
REST API, but unfortunately it does not returns important information such
as the URL of the file.

To keep in line with Bioconductor recommendations and users expectations
(i.e.: Dario Strbenac response), I won't update the metadatas in the
Release branch. I'll point to the devel branch and to the function
available to download a new version of `encode_df` locally.

Thank you for the clarifications,
Charles Joly Beauparlant.

On Thu, May 26, 2016 at 8:37 PM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:

> Hi Charles,
> Yes, the usual advice is that you touch release for bug fixes only but
> can update as often as you like in devel. This is the same pattern
> followed for our experimental data and annotation packages. Once we have
> a release those data are frozen and for 6 months are considered the
> 'current release'.
> Are the ENCODE files updated more frequently than every 6 months? I was
> wondering if you could query for this information on-the-fly but a quick
> look at encode_df makes me think the data are heavily curated and
> real-time retrieval might not be possible.
> Valerie
> On 05/22/2016 06:36 AM, Charles Joly wrote:
> > Hello,
> >
> > I'm the maintainer of the ENCODExplorer package. We provide the metadatas
> > of the ENCODE project files in the `data/` section of the package.
> >
> > The problem is that there are regularly new datasets and changes in the
> > previous dataset. I was wondering if it is OK to push new versions of the
> > metadatas even if the documentation mentions:
> > "Only bug fixes should be back-ported to the release branch. This is so
> > that users of the release branch have a stable environment in which to
> get
> > their work done."
> >
> > Thanks!
> > Charles Joly Beauparlant.
> >
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> >
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