[Bioc-devel] Bioconductor Git/GitHub Mirrors

[Robert M. Flight]

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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