[Bioc-devel] Fixing bugs in release version

Thu Jul 12 17:12:42 CEST 2018

Eugenia,

The easiest way to see the logs for git.bioc master branch is to look here: http://bioconductor.org/developers/gitlog/. They have an RSS feed for both the master and release branch as well. Since I don’t use RSS I instead did the following:

1) cloned your repo from git.bioc: git clone https://git.bioconductor.org/packages/Onassis
2) Use git fetch to allow me to checkout the RELEASE_3_7 branch: git fetch
3) Checked out the RELEASE_3_7 branch: git checkout RELEASE_3_7
4) Then looked at the commit history: git log

The latest commit (at the top) is ce0fb68.
5) If I look at the DESCRIPTION file: less DESCRIPTION
it shows Version: 1.2.1.

I believe this is correct, although, I am not an expert either. Maybe someone will chime in and confirm that I am giving you the correct procedure.

On the RELEASE_3_7 branch in your Github repo (not git.bioc) I can see that the version was changed from 1.2.1 to 1.3.1 in the most recent commit (def6111) here: https://github.com/eugeniaeueu/Onassis/commit/def6111f80db3ed03a991416ce724425d2027d01… but, as far as I can tell, you have not pushed that commit to git.bioc and, therefore, the version on git.bioc is correct (1.2.1).

Hope this was somewhat helpful.

Kind Regards,
Jason

On 12 Jul 2018, at 16:51, Eugenia Galeota <eugenia.galeota using gmail.com<mailto:eugenia.galeota using gmail.com>> wrote:

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<http://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<mailto: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<mailto:grimbough using gmail.com>> wrote:

Hi Jason,

There is no explicit connection between Github and git.bioconductor.org<http://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<http://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<mailto: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<mailto: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<mailto: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<mailto: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>
>>
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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<mailto:eugenia.galeota using iit.it>
Tel: +39 02 9437 5046
Via Adamello 16, 20139 Milan, Italy

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