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

Thomas Sherman t@herm@4 @ending from jhu@edu
Thu Jun 14 01:16:49 CEST 2018

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.


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