[Bioc-devel] Bioconductor-mirror permanently removed August 25th

[Shepherd, Lori]

Even before the bioconductor git server, when we still were using svn, users were confused at where to make updates and push changes.  Now even more so we have seen several packages try and push to the bioconductor-mirror or change the remotes to point the the mirror locations.  It has created a lot of confusion.




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org>
Sent: Wednesday, September 6, 2017 11:21:34 AM
To: Jim Hester
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Bioconductor-mirror permanently removed August 25th

Hi Jim

We are more worried about the confusion it creates among the users.

Users have tried to push their commits to the bioconductor-mirror instead of the bioconductor git server. Another source of confusion is, some maintainers have forked their packages from the Bioconductor-mirror, and have started developing from that point on GitHub. This creates a unique issue of duplicate commits, when they merge updates from the bioc-git server. People also send in pull requests/issues to this mirror repositories where they are unmaintained, causing a new kind of problem to both users and maintainers.

We realize the importance of a browsable source repository, and are looking into gitweb on the bioc-git server directly. Having a GitHub based mirror also prevents us from hosting data-packages on Github. The idea of a browsable source should be to view all Bioconductor packages( software / data / workflows). My vote is to remove this, only because of the amount of confusion it causes on the regular.

I’ll let others chime in as well, and would love to hear your thoughts about Gitweb(https://git-scm.com/docs/gitweb) or other such software.


Best,

Nitesh

> On Sep 6, 2017, at 11:07 AM, Jim Hester <james.f.hester at gmail.com> wrote:
>
> This mirror could be relatively simply supported by setting up an additional remote in the server side repositories and adding a post-receive hook to each repository that simply pushes to the GitHub mirror remote after commits are received.
>
> https://git-scm.com/book/gr/v2/Customizing-Git-Git-Hooks
> https://help.github.com/articles/about-github-mirrors/
>
> Having an easily browsable source repository online is a pretty valuable thing, it is a shame to lose this.
>
> Jim
>
> On Thu, Aug 17, 2017 at 3:53 PM, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org> wrote:
> Hi Maintainers,
>
> The https://github.com/Bioconductor-mirror is now stale after Bioconductor’s git transition. We are no longer going to support it, and will be taking it offline permanently on August 25th (next Friday).
>
> If you have “forked” a repository from the Bioconductor-mirror, you will be fine. It will not have any consequence on your repository, the only change will be the “forked from bioconductor-mirror” tag will be removed.
>
>
> Best,
>
> Nitesh
>
>
>
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