[Bioc-devel] Fixing bugs in release version

[Mike Smith]

Hi Jason,

There is no explicit connection between Github and git.bioconductor.org
(I'm going to call this git.bioc from now on)  Only changes that are pushed
to git.bioc will be reflected in the packages available via
www.bioconductor.org and biocLite().  You can make any changes you like to
a repo on Github and similarly create branches with any name you want, but
this is completely separate from Bioconductor.  Having a  RELEASE_X_Y
branch on Github and making a change there does not automatically mean it
gets sent to git.bioc.

Many people like to maintain a Github repository in addition to git.bioc as
it provides many useful features for social coding (comments, issues, text
search etc) but it's entirely possible to ignore Github completely after
your package has been accepted.

It sounds like you're interested in using both git.bioc and Github, in
which case the instructions at
https://bioconductor.org/developers/how-to/git/push-to-github-bioc/ might
help with keeping them in sync.

Mike

On Thu, 12 Jul 2018 at 11:53, Jason Serviss <jason.serviss using ki.se> wrote:

> Mike,
>
> It would appear that the version on Eugenia’s RELEASE_3_7 branch on her
> git repo is 1.3.1 (
> https://github.com/eugeniaeueu/Onassis/commit/def6111f80db3ed03a991416ce724425d2027d01)
> so why is it 1.2.1 on the Bioconductor repo?
>
> p.s. have recently been struggling with a similar issue so, just asking to
> try to get a better understanding
>
> Kind Regards,
> Jason
>
> > On 12 Jul 2018, at 11:12, Mike Smith <grimbough using gmail.com> wrote:
> >
> > It looks to me like you have made the changes correctly.  When I checkout
> > your packages you have versions 1.3.1 and 1.2.1 for the master and
> > RELEASE_3_7 branches respectively.
> >
> > -> % git checkout --quiet master && cat DESCRIPTION | grep Version
> > Version: 1.3.1
> >
> > -> % git checkout --quiet RELEASE_3_7 && cat DESCRIPTION | grep Version
> > Version: 1.2.1
> >
> > The reason it still says 1.2.0 on the landing page is that there can be
> > delay before changes in the git repository propagate to the home pge.
> You
> > can check the last time a snapshot of your packages was taken on
> > http://bioconductor.org/checkResults/release/bioc-LATEST/Onassis/ For
> you
> > this was Snapshot Date: 2018-07-10 16:46:08 -0400 (Tue, 10 Jul 2018)
> which
> > is before your commit with the version bump.  It would expect the change
> to
> > propagate through sometime today.
> >
> > Mike
> >
> > On Thu, 12 Jul 2018 at 10:52, Eugenia Galeota <eugenia.galeota using gmail.com
> >
> > wrote:
> >
> >> Good morning,
> >> I'm writing because I tried to fix some bugs in the current release
> version
> >> of my package Onassis.
> >> I followed these instructions (
> >>
> >>
> https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
> >> )
> >> but maybe I messed up with the version in the DESCRIPTION file. In the
> >> Bioconductor page RELEASE_3_7
> >> https://www.bioconductor.org/packages/3.7/bioc/html/Onassis.html
> Onassis
> >> has 1.2.0 version, while actually in the repository I don't know how I
> am
> >> at version 1.3.1 (shouldn't it be a development version?).
> >> Will my bug fixes be available in the RELEASE_3_7 to users installing
> the
> >> package?
> >>
> >> I thought that Onassis version after the bug fixes, should have been
> 1.2.1.
> >> Is that correct? How can I update just the current Onassis package in
> >> RELEASE_3_7 (the current one) ?
> >> Thanks Eugenia
> >>
> >> --
> >> Eugenia Galeota, PhD
> >> Center for Genomic Science of IIT using SEMM
> >> Computational Epigenomics
> >> Email: eugenia.galeota using iit.it
> >> Tel: +39 02 9437 5046
> >> Via Adamello 16, 20139 Milan, Italy
> >>
> >>        [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

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