Development

Rebuild the NAMESPACE and documentation with:

library(devtools)
document()

Note that there's an issue with having the entab dependency in the R bindings as a path (and including this in the workspace in the directory above) because R will only build this directory and not include the parent directory. This will cause the build process to fail with a message about "could not find entab, only entab-r". What this means in practice is that a new version of entab needs to be pinned in Crates before any new features can be used in here.

For future inspiration: There's an example Windows build config that might be good inspiration for building/releasing this for Windows machines. gifski is one of the few packages on CRAN with a Rust build pipeline.

Installation

Build the R package itself with:

R CMD INSTALL .

You can also install off of Github with:

library(devtools)
devtools::install_github("bovee/entab", subdir="entab-r")

Additional instructions for Mac OS X installation

If you're using RStudio on a Mac, you will likely need to tell R Studio where to find cargo (the Rust package manager) by adding it to your path. You can do this by modifying your .Rprofile file as suggested below:

1. Find your .Rprofile file in your home directory (you may need to press Command + Shift + period to reveal hidden files) and open it in your text editor of choice. Alternatively, you can call usethis::edit_r_profile() from RStudio to automatically open your .Rprofile.
2. Add Sys.setenv(PATH = paste0("/Users/<user>/.cargo/bin:", Sys.getenv("PATH"))), replacing with your username. This will append Cargo to your path when you open RStudio.
3. Save your .Rprofile and restart R Studio.
4. Install Entab from GitHub.

Usage

And then use:

library(entab)
r <- Reader('../test_file.fasta')
data <- as.data.frame(r)