[Bioc-devel] Bioconductor Git/GitHub Mirrors

Jim Hester james.f.hester at gmail.com
Fri Jun 19 17:19:04 CEST 2015 

I think these are unavoidable artifacts with the current setup.  The
commits from the Bioconductor-mirror are coming from SVN after being
translated so they have extra metadata attached to the commit message,
while your original commits do not have this.  Therefore GitHub cannot
properly disambiguate the two commits, and you get this message.  You will
also notice you get the same commit twice in your log (
https://github.com/rmflight/categoryCompare/commits/master) due to the same
reason.

Using your own repo instead of forking Bioconductor-mirror will make the
message go away and you should also not have the issue with double commits
I believe.

On Fri, Jun 19, 2015 at 10:23 AM, Robert M. Flight <rflight79 at gmail.com>
wrote:

> So this seems to work quite nicely. But in my own testing of committing
> with my categoryCompare package, there is one interesting issue of Github
> complaining about how many commits ahead / behind the fork is.
>
> So I moved my old github repo, and then made a fresh fork from the
> Bioconductor mirror, and made a new clone of that fork on my local machine,
> and ran update_remotes.sh.
>
> Made some changes to the readme (pointing to personal repo for issues) and
> committed in *master
>
> git push origin master (push back up to my personal copy)
> git checkout devel
> git svn rebase
> git merge master --no-edit
> git svn rebase && git svn dcommit --add-author-from
>
> When I looked at my personal fork, it shows 1 commit ahead & behind the
> original. So I pulled from *bioc* remote into master (and merge it), and
> then pushed back up to master.
>
> I still have this message: This branch is 2 commits ahead of
> Bioconductor-mirror:master, but there are no file differences.
>
> Does anyone know how to make this message go away? Should I just use my
> own repo instead of a *fork* of the Bioconductor-mirror?
>
> -Robert
>
>
> On Wed, Jun 17, 2015 at 10:10 AM Jim Hester <james.f.hester at gmail.com>
> wrote:
>
>> I have (in the past couple of minutes) added a more detailed description
>> to all of the GitHub pages.  If you have URL or BugReports fields in your
>> package DESCRIPTION those are used to provide links to the project page and
>> bug tracker if they are available, see Roberts
>> https://github.com/Bioconductor-mirror/categoryCompare for an example.
>>
>> I would also recommend doing as Robert suggests and adding a link in a
>> README.md file if you would like to direct users elsewhere.  These files
>> are automatically rendered by GitHub and users are used to looking at them
>> for project documentation.
>>
>> Thank you all for being patient as we roll out this functionality.
>>
>> Jim
>>
>> On Wed, Jun 17, 2015 at 9:06 AM, Robert M. Flight <rflight79 at gmail.com>
>> wrote:
>>
>>> Why not write your own *readme.md* file for the package and put the link
>>> there? There is nothing stopping the maintainer from having a README file
>>> in the package. Although it does not show up on the Bioconductor page, it
>>> shows up nicely on Github:
>>>
>>> My package:
>>>
>>> https://github.com/Bioconductor-mirror/categoryCompare
>>> https://github.com/rmflight/categoryCompare
>>>
>>> -Robert
>>>
>>> On Wed, Jun 17, 2015 at 8:43 AM Michael Lawrence <
>>> lawrence.michael at gene.com>
>>> wrote:
>>>
>>> > It would be cool if we could somehow get the equivalent of the
>>> > bioconductor package page to show up as the "readme" on the github
>>> > page. Or at least, if there could be a very obvious link from the
>>> > mirror repository to the maintainer repository, without having to
>>> > click through to the Bioconductor package page, which might confuse
>>> > new users a bit.
>>> >
>>> >
>>> > On Tue, Jun 16, 2015 at 12:00 PM, Dan Tenenbaum <
>>> dtenenba at fredhutch.org>
>>> > wrote:
>>> > > Dear Bioconductors,
>>> > >
>>> > > We're pleased to announce the availability of Bioconductor Git
>>> Mirrors.
>>> > > These are read-only GitHub repositories (available under
>>> > https://github.com/Bioconductor-mirror)
>>> > > for every Bioconductor software package. These repositories are
>>> > synchronized with our
>>> > > Subversion repository. Package maintainers (or anyone else) can fork
>>> > these repositories
>>> > > and do their development on the fork. Complete documentation of the
>>> > mirrors is at
>>> > >
>>> > > http://bioconductor.org/developers/how-to/git-mirror/
>>> > >
>>> > > These mirrors supersede the Git-SVN bridge, which is now deprecated.
>>> > > Creation of new bridges is disabled and maintainers who are using the
>>> > bridge
>>> > > should migrate to the Git mirrors as soon as it's convenient, as the
>>> > bridge
>>> > > will eventually go away. Instructions for migrating can be found at
>>> the
>>> > above link.
>>> > >
>>> > > Some features of the new Git Mirrors, and why we feel they are a
>>> better
>>> > solution than the Git-SVN bridge:
>>> > >
>>> > >  - The mirrors contain complete commit history.
>>> > >  - The mirrors contain release branches for Bioconductor 3.0 and
>>> 3.1, and
>>> > >    new releases will be added as they happen. You will no longer need
>>> > >    separate repositories for release and devel.
>>> > >  - Setup is easy and you no longer have to grant any permissions on
>>> your
>>> > >    repository to other users. You can commit directly to Subversion
>>> > >    using git-svn (https://git-scm.com/docs/git-svn).
>>> > >  - Each git commit appears in the SVN log as a distinct SVN commit;
>>> > commits
>>> > >    are no longer grouped together as they were with the bridge. Each
>>> git
>>> > >    commit can be mapped to a specific svn commit, and vice versa.
>>> > >  - The Git mirrors are much more reliable.
>>> > >  - Use is flexible. You can use git locally (without GitHub) or you
>>> > >    can use GitHub as well, to take advantage of all its social coding
>>> > features.
>>> > >  - Using GitHub's code search, you can search the entire Bioconductor
>>> > codebase.
>>> > >    Here's a sample search: https://goo.gl/jI92Ys
>>> > >  - Subversion is fully supported and remains the cannonical
>>> repository;
>>> > use
>>> > >    of Git and GitHub is optional.
>>> > >
>>> > > We are excited about these new mirrors (brought to you by the hard
>>> > > work of Jim Hester) and we hope you are too. Questions and comments
>>> are
>>> > > welcome on the bioc-devel mailing list.
>>> > >
>>> > > Dan
>>> > >
>>> > > _______________________________________________
>>> > > Bioc-devel at r-project.org mailing list
>>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> >
>>> > _______________________________________________
>>> > Bioc-devel at r-project.org mailing list
>>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> >
>>>
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>>
>>
>>>
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>>

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