Importing plink pgen/pvar support from pgenlibr into other R packages at the the C++ level

[GabrielHoffman]

Thank you for plink2 and the pgenlibr library.

I am writing an R package that uses an Rcpp backend for analysis, I would like to add support for plink pgen/pvar files. One option is to copy the code from the pgenlibr/src into my own package. But this 1) requires manual updates when pgenlibr changes and 2) doesn't address the issue for other package developers.

But there is an easy fix. Files in inst/include are retained in the path to the installed R package (code in src is not). This allows a package developer to link to C/C++ code distributed by other R packages.

In the pgenlibr package, this just involves moving the symlinks to include/, libdeflate/, simde/, and zstd/ from src/ to inst/include/. And updating the Makefile to include -I../inst/include/.

I tried it and it works great. Would you be interested in this update or including a merge request?

Best,
Gabriel

[chrchang]

Sure, that update sounds reasonable.