[Bioc-devel] Including a submodule in the main package repository

Turaga, Nitesh Nite@h@Tur@g@ @ending from Ro@wellP@rk@org
Mon Jun 18 17:30:50 CEST 2018

Hi Tom,

I agree with Kasper. It is far easier to maintain two repos and sync with your Bioconductor package as needed. We have no protocols in place or documentation in place to support submodules at the moment.

I also want to add that your setup on GitHub is up to you as a maintainer and developer. As long as the repository on the Bioconductor server has all the required files to build and make your package work as expected.

I’ll explore submodules a little more and get back to you.



> On Jun 14, 2018, at 3:01 AM, Kasper Daniel Hansen <kasperdanielhansen using gmail.com> wrote:
> My opinion: maintain two repos and pull/push between them. You would want
> the ability to have them out of sync anyway.
> Best,
> Kasper
> On Thu, Jun 14, 2018 at 1:16 AM, Thomas Sherman <tsherma4 using jhu.edu> wrote:
>> Hi all,
>> I'm a developer for the CoGAPS package (https://github.com/FertigLab/
>> CoGAPS). I'm looking into ways to build our core C++ code as a standalone
>> application and I would like to be able to maintain a single repository for
>> the C++ code and pull that into both repositories for the R package and
>> standalone application. It seems the easiest way to do this would be to
>> have a git submodule in the R package repository that refers to the C++
>> code. However, based on this comment (https://github.com/
>> Bioconductor/Contributions/issues/459#issuecomment-376671397) it seems
>> that is not the desired configuration.
>> The best alternative I can think of would be to provide a separate library
>> for our core algorithm and then link against that in both the R package and
>> standalone version. In this case, we would have to provide instructions for
>> downloading and building the library - which seems like more work for the
>> end user than if everything was included with a submodule.
>> I'm wondering if the first approach using a submodule would be possible,
>> and if not, has anyone ran into this issue before and found a nice solution.
>> Thanks,
>> Tom
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