[Bioc-devel] A little confuse about how to update accepted package

Kasper Daniel Hansen k@@perd@nielh@n@en @ending from gm@il@com
Sat Nov 10 15:16:06 CET 2018


The night before the release your package was at 0.99.x in the devel branch

At release, two things happened:
  the package was added to the release branch with version 1.0.0
  the package in the devel branch was updated to version 1.1.0

So basically version 0.99.19 == 1.0.0 == 1.1.0. And basically after release
all packages gets bumped two version numbers.  Note that in x.y.z, "y" is
odd = devel, "y" is even = release.

Usually you should not update the release branch (version 1.0.0) unless
there are critical bug fixes.  Any update in the release branch should be
associated with an email to bioc-devel according to project policies
(although this is unfortunately often not done).

Most likely you should just continue working on version 1.1.0


On Sat, Nov 10, 2018 at 6:10 AM Martin Morgan <mtmorgan.bioc using gmail.com>

> The steps below are correct, but perhaps not sufficient for what you want
> to do.
> Bioconductor packages consist of release branches, which are meant to be
> stable for the end user, and the 'devel' branch where new features can be
> introduced.
> There is a version numbering scheme, outlined at
>   http://bioconductor.org/developers/how-to/version-numbering/
> to ensure that each published version of the package has a different
> version, that versions in release always increase, and that the devel
> version is always ahead of the release version. For your package, the
> release version is 1.0.0, and the devel version is 1.1.0.
> If you intended to make a change to the devel version of your package,
> because you were introducing a new feature or perhaps testing a bug fix,
> then you have been successful; you have pushed your changes to the devel
> ('master') branch, and incremented the version to 1.1.1.
> If you intend to make this change also in the release, then the extra
> steps in
> http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
> are required -- check out the RELEASE_3_8 branch, port your changes from
> master, increment the release version to 1.0.1, and push.
> During the submission process packages are built immediately, but in the
> devel and release branches they are built nightly, approximately (I think
> that last night in particular there were issues with network connectivity
> that might severely limit the success of the build). The build reports are
> available from
>   http://bioconductor.org/checkResults/
> note the 'snapshot' time stamps and commit information for the overall
> build and for your individual package to see whether your commit was
> included in the nightly build.
> Martin
> On 11/10/18, 5:53 AM, "Bioc-devel on behalf of Tang, Wenhao" <
> bioc-devel-bounces using r-project.org on behalf of wenhao.tang15 using imperial.ac.uk>
> wrote:
>     Dear Bioconductor team,
>     My package bayNorm has recently been accepted, it now has version
> 1.0.0. Currently I would like to make some changes to it. I look through
> the tutorials online but I am still very confused. Below is what I have
> done:
>     My local repository has version 0.99.19. So I  did the following in my
> local repository:
>       1.  git remote add upstream git using git.bioconductor.org:
> packages/bayNorm
>       2.  git fetch --all
>       3.  git checkout master
>       4.  git merge origin/master
>       5.  git merge upstream/master
>     Now the local version is 1.1.0 rather than 0.99.19.
>     Then I just did a small change (in addition, I bump the version to
> 1.1.1) and then run the following command under the local repository:
>       1.  git push upstream master
>       2.  git push origin master
>     Is the above procedure correct? Will I see the package building report
> like what I have received during the submission process?
>     Your tutorials are very clear, and I am sorry if my question is too
> trivial.
>     Thank you very much!
>     Best wishes,
>     Wenhao
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