create R package

[adokter]

adokter/bioRad#156 requires compilation of vol2bird within R, instead of accessing it through Docker.

To keep code bases separate, I suggest making an R-package for vol2bird that will be a dependency to bioRad (instead of integrating vol2bird C-code itself into bioRad)

R documentation for how to include external code:
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Non_002dR-scripts-in-packages

Hadley Wickham's tutorial on compiled code:
http://r-pkgs.had.co.nz/src.html

Examples of R packages based on C/C++ code:

• xgboost
• Rhdf5lib
• tibble

Required steps:

• define git submodules for all library dependencies used by vol2bird. Note that we will need to install a package with submodules using install_git with args="--recursive" instead of install_github.
• define configure and cleanup scripts, see https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Configure-and-cleanup
• rewrite vol2bird's Makefile into an R-compatible Makevars file
• (need to check) register library functions we want to use in R, see CRAN manual and xgboost for examples. This seems also the process by which packages can share compiled code, e.g. see how rhdf5 uses Rhdf5lib
• check whether we can use hlhdf from Rhdf5lib: no, nomenclature seems different when checking shared library contents with nm
• link to a proj4 library from an existing R-package, potentially proj4 (https://github.com/s-u/proj4/ and http://www.rforge.net/proj4/)
• compile hlhdf while linking to Rhdf5lib base hdf5 library in R
• compile rave (depends on hdf5, hlhdf) in R package
• compile iris2odim in R package
• compile rsl in R package
• compile / link to gsl in R package, see RcppGSL
• compile / link to libconfuse in R package
• compile / link to PyTorch, potentially through R packages rTorch (https://github.com/f0nzie/rTorch) or torch (https://dfalbel.github.io/torch/)
• compile vol2bird in R package

[adokter]

See this discussion of submodules. There is also a lot of criticism of submodules out there.

[adokter]

For Windows compilation, need to find out if we can cross-compile using Rtools

[bart1]

Quick update I have been able to make a small toy package that converts files, it though still depends on the libvol2bird.so file, lets see if i can include the source

[bart1]

I just got a version working where the library is compiled directly into the r package. It might still be a challenge to get it cran compatible but it works well. I will upload it later today

[bart1]

Here is a quick mockup: https://github.com/bart1/Rvol2bird it is only tested on linux, and mostlikely does not directly compile on other OS's. Currently copies of the required libraries are included (no git subtrees). So it does not follow changes in the libaries

[adokter]

Asked Simon Urbanek about proj4 header files in s-u/proj4#6

proj4 C library not available via proj4 package

[adokter]

See adokter/bioRad#385 and https://docs.ropensci.org/rnoaa/ to read NOAA data into R directly. Unfortunately NEXRAD level2 and level3 data are currently not supported