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

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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