[Bioc-devel] git push to devel versions

James W. MacDonald jmacdon at uw.edu
Wed Oct 11 18:20:38 CEST 2017

On Wed, Oct 11, 2017 at 2:02 AM, Samuel Wieczorek <samuel.wieczorek at cea.fr>

> Hi all,
> The new release of Bioconductor is coming soon and I would like to be
> sure that I am doing the right things with Git.
> I am a bit confused with the Git commands to use in order to update the
> devel versions of my packages Prostar and DAPAR and DAPARdata (which is
> an experimentData package).
> Can you (re)explain to me the different steps are required and where to
> push my updates (origin ? upstream ? RELEASE_3_5 ?) ?

You should almost never push to the RELEASE_3_5 branch; that's the current
release, and unless you are fixing an obvious bug you should Just Leave It
Alone. The rationale for that stance is that people often want their
analyses to be reproducible. If you are constantly pushing changes, then it
could make it difficult for your users to reproduce existing research
(because they can't easily get the version they used).

Nitesh gave a really nice talk about using Git at the recent Bioconductor
meeting. You can get the slides here:

There is also a page on Bioconductor (
https://www.bioconductor.org/developers/how-to/git/) that covers lots of

As to whether or not you push to origin or upstream, that depends on
whether or not you have your package on GitHub. Which is covered in the
documentation I have pointed out.



> Thanks
> Cheers
> Sam
> --
> *Samuel Wieczorek
> Etude de la Dynamique des Protéomes (EDyP)*
> *Laboratoire Biologie à Grande Echelle (BGE)*
> *U1038 INSERM / CEA / UGA*
> *Biosciences and Biotechnology Institute of Grenoble (BIG)*
> *CEA / Grenoble*
> *17 avenue des Martyrs*
> *F-38054 Grenoble Cedex 9*
> */Tél. :*
> */Fax :*
> http://www.edyp.fr/
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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