https://github.com/luizirber/sourmash-r
An experiment on wrapping sourmash Rust code and calling it in R
https://github.com/luizirber/sourmash-r
sourmash
Last synced: 7 months ago
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An experiment on wrapping sourmash Rust code and calling it in R
- Host: GitHub
- URL: https://github.com/luizirber/sourmash-r
- Owner: luizirber
- License: other
- Created: 2019-05-17T17:28:41.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2019-05-17T17:54:55.000Z (over 6 years ago)
- Last Synced: 2025-03-15T14:56:45.048Z (7 months ago)
- Topics: sourmash
- Language: C
- Homepage:
- Size: 4.88 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# sourmash-R
[](https://travis-ci.com/luizirber/sourmash-r)
[](https://ci.appveyor.com/project/luizirber/sourmash-r)
> An experiment on wrapping sourmash Rust code and calling it in R
Rust is a modern alternative to C and compiled rust code is ABI compatible with C. Many Rust libraries include C API headers so that the compiled rust code can be called from R/C/C++ as if it were C code.
The [r-rust](https://github.com/r-rust) organization contains several example R packages interfacing with Rust. Also have a look at the [slides](https://jeroen.github.io/erum2018/) about this project presented at eRum2018!
This example is based on the [hellorust](https://github.com/r-rust/hellorust) example project.
## Cargo
The standard rust toolchain includes a great package manager `cargo` with a corresponding registry [crates.io](https://crates.io/). Cargo makes it very easy to build a rust package including all dependencies into a static library that can easily be linked into an R package.
This is perfect for R because we can compile and link all rust code at build-time without any system dependencies. Rust itself has no substantial runtime so the resulting R package is entirely self contained. Indeed, rust has been designed specifically to serve well as an embedded language.
## Package Structure
```
sourmash-r
├─ configure ← checks if 'cargo' is installed
├─ src
│ ├─ sourmash ← git submodule with dib-lab/sourmash content
│ │ ├─ Cargo.toml ← cargo dependencies and metadata
│ │ ├─ src ← rust source code
│ │ └─ include
│ │ └─ sourmash.h ← C headers for exported rust API
│ ├─ Makevars ← Ties everything together
│ └─ wrapper.c ← C code for R package
├─ DESCRIPTION
└─ R ← Standard R+C stuff
└─ sourmash.R
```
## Installation
Note that `cargo` is only needed at __build-time__. Rust has __no runtime dependencies__. To install on MacOS use homebrew:
```
brew install rust
```
And on Debian/Ubuntu:
```
sudo apt-get install cargo
```
And on Fedora / CentOS:
```
sudo yum install cargo
```
And on Arch:
```
sudo pacman -Sy cargo
```
On CentOS you first need to enable EPEL via `sudo yum install epel-release`.
### Windows
In order for rust to work with R you need to install the toolchain using `rustup` and then add the `x86_64-pc-windows-gnu` and `i686-pc-windows-gnu` targets. First download [rustup-init.exe](https://win.rustup.rs/) and then install the default toolchain:
```
rustup-init.exe -y --default-host x86_64-pc-windows-gnu
```
To compile 32bit packages also add the i686 target:
```
rustup target add i686-pc-windows-gnu
```
The [appveyor.yml](appveyor.yml) file shows this live in action. For more information about rust on Windows see [here](https://github.com/rust-lang-nursery/rustup.rs/blob/master/README.md#working-with-rust-on-windows).
## Resources
- Erum2018 [slides](https://jeroen.github.io/erum2018/) about this project presented by Jeroen
- [Rust Inside Other Languages](https://doc.rust-lang.org/1.6.0/book/rust-inside-other-languages.html) chapter from official rust documentation
- [rustr](https://rustr.org/) is a Rust library that provides a Rust API to work with R.
- Duncan's proof of concept: [RCallRust](https://github.com/duncantl/RCallRust)