[Bioc-devel] Fixing bugs in release version

Thu Jul 12 16:51:19 CEST 2018

Before the bug fixes I was just working on a master and devel branch on my
Github connected with bioconductor repository (through upstream). When I
decided to fix some of the bugs in the release version I just followed the
instructions in the page that I linked in the first message. It's when I
also created the RELEASE_3_7 branch in my git repository. After that, in
one of the commits I noticed that the version in the DESCRIPTION file
changed to 3 (but I can't remember how it happened, that's why I wrote that
maybe I messed up with the DESCRIPTION file) and when I tried to change it
back to 2 git returned an error message saying that it's impossible to bump
older versions:

host016:Onassis egaleota$ git status

On branch RELEASE_3_7

Your branch is ahead of 'upstream/RELEASE_3_7' by 1 commit.

  host016:Onassis egaleota$ git checkout master

Switched to branch 'master'

Your branch is ahead of 'origin/master' by 1 commit.

  (use "git push" to publish your local commits)

host016:Onassis egaleota$  git push upstream master

Counting objects: 5, done.

Delta compression using up to 8 threads.

Compressing objects: 100% (5/5), done.

Writing objects: 100% (5/5), 2.33 KiB | 2.33 MiB/s, done.

Total 5 (delta 3), reused 0 (delta 0)

remote: Error: Illegal version bump from '1.3.0' to '1.2.1'. Check

remote: http://bioconductor.org/developers/how-to/version-numbering/

remote: for details

To git.bioconductor.org:packages/Onassis.git

Anyway, since I'm not an expert, I have another simple question. Where can
I find the commit logs in git.bioc? I usually looked at git logs on my
local machine with the command "git logs" but the commit ids (

commit 629cb9c4c34b82866c11b14dc2972fedc163c411) are different from those
used by Jason ((ce0fb68)).

Thank you for this discussion.

Eugenia

2018-07-12 16:20 GMT+02:00 Jason Serviss <jason.serviss using ki.se>:

> Mike,
>
> Thanks for your reply. I understand that there is no “automatic syncing”
> between Github and git.bioc and that changes made on Github need to be
> explicitly pushed to git.bioc to be reflected in the packages available via
> biocLite. Although, it would seem as though, from Eugenia’s original
> question, her intentions were to make a change in Github on the release
> branch and then transfer those changes to git.bioc. After looking a bit
> more carefully, it would seem that Eugenia’s last commit on git.bioc
> (ce0fb68) indeed has version 1.2.1 although in her Github repo she has made
> on subsequent commit where she changed the version back to 1.3.1 (def6111).
> Makes perfect sense then… I should have looked a bit more closely initially.
>
> Regards,
> Jason
>
>
>
> On 12 Jul 2018, at 14:58, Mike Smith <grimbough using gmail.com> wrote:
>
> 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
>> <https://maps.google.com/?q=Via+Adamello+16,+20139+Milan,+Italy&entry=gmail&source=g>
>> >>
>> >>        [[alternative HTML version deleted]]
>> >>
>> >> _______________________________________________
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>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>
>> >
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>> >
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>>
>>
>

-- 
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

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