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

Kasper Daniel Hansen k@@perd@nielh@n@en @ending from gm@il@com
Thu Jun 14 09:01:51 CEST 2018

My opinion: maintain two repos and pull/push between them. You would want
the ability to have them out of sync anyway.


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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