Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/r-hub/sysreqsdb

SystemRequirements mappings for R packages
https://github.com/r-hub/sysreqsdb

r rstats

Last synced: 2 months ago
JSON representation

SystemRequirements mappings for R packages

Awesome Lists containing this project

README 

        

## This repository is now archived in favor of https://github.com/rstudio/r-system-requirements



# sysreqs



> SystemRequirements for R packages



## Superseded!



This project is replaced by a new database [rstudio/r-system-requirements](https://github.com/rstudio/r-system-requirements), which is used by `pak` and `rhub2`.  



## Introduction



Many R packages require system libraries or other external software to build

or run. The `SystemRequirements` field in the package `DESCRIPTION` file should

declare these dependencies, as free form text. This makes it difficult to

automate building and checking of R packages, since we need to guess which

software should be installed on the build machine.



The `sysreqs` project formalizes these requirements, and provides a database

with API to quickly find out which Homebrew, Debian, Ubuntu, RHEL/Centos, etc

packages or other software needs to be available to build and use R packages.



In this README:



* [supported platforms](#supported-platforms)

* [the database format](#database-format)

* [how to contribute](#contributing)

* [how to access the data](#database-access)

* [where the `sysreqs` project is used](#use-cases-of-the-database)



## Supported platforms



Distributions using `deb` package format:

* Ubuntu Linux

* Debian Linux



Distributions using `rpm` package format:

* Fedora Linux (recent releases)

* RedHat and CentOS Linux (recent releases)



Distributions using the `PKGBUILD` package format:

* Arch Linux



Non-native package formats:

* HomeBrew package manager on MacOS

* Pacman/Rtools on Windows (forthcoming)



## Database format



The `sysreqs` database is a JSON document store. Each document contains

mappings for a single canonical system requirement. It contains both

the mappings to `SystemRequirements` fields, and platform dependent packages

or URLs.



Below an example to make this clear. Several R packages require the libxml2

library. For building these packages from source, the libxml2 development

headers are needed as well. The R packages refer to libxml2 in different

ways. E.g. [`igraph`](https://cran.r-project.org/web/packages/igraph/index.html) has simply `libxml2` and [`XML`](https://cran.r-project.org/web/packages/XML/index.html) has `libxml2 (>= 2.6.3)`

in their `SystemRequirements` fields.



```json

{

  "libxml2": {

    "sysreqs": "libxml2",

    "platforms": {

       "DEB": "libxml2-dev",

       "OSX/brew": null,

       "RPM": "libxml2-devel"

    }

  }

}

```



Some notes:

* The `sysreqs` field can be a string or array, and its entries can be fixed

  strings or regular expressions (when starting and ending with a forward slash, only [JavaScript RegExp](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/RegExp) are supported. [Example of a list `sysreqs` field](https://github.com/r-hub/sysreqsdb/blob/9c0acc932a11b1eb9f1600e27ca39a4d7deb0425/sysreqs/cairo.json#L3), [example of a `sysreqs` field with a regular expression](https://github.com/r-hub/sysreqsdb/blob/9c0acc932a11b1eb9f1600e27ca39a4d7deb0425/sysreqs/imagemagick.json#L3).

* Not all platforms have the same information, For `DEB` based Linux

  flavours (Debian, Ubuntu, etc.) packages that can be installed via the

  host package manager are listed: [`DEB` line example](https://github.com/r-hub/sysreqsdb/blob/9c0acc932a11b1eb9f1600e27ca39a4d7deb0425/sysreqs/cmake.json#L5). For Windows, typically URLs that have

  to be downloaded and installed: [Windows lines example](https://github.com/r-hub/sysreqsdb/blob/9c0acc932a11b1eb9f1600e27ca39a4d7deb0425/sysreqs/cmake.json#L8).

* `null` for `OSX/brew` means that nothing is needed, the system includes

  the requirement(s) by default. [Example](https://github.com/r-hub/sysreqsdb/blob/92ab711e2ddd5aa8ebb93f6a1fdc1d2b9012bc75/sysreqs/libbi.json#L5).



## Database access



See API docs at 



## Contributing



Your contributions are welcome! More details below.



### Adding or completing entries



Please read about [the data format](#database-format) first. Entries should be added or improved via pull requests.



* If a package (of yours or not) has a dependency that's not listed here yet, open a pull request to add it. You don't need to have it mapped to all platforms yet. [Example of such a PR](https://github.com/r-hub/sysreqsdb/pull/46).



* You can also make a pull request to add a mapping to a platform. [Example of such a PR](https://github.com/r-hub/sysreqsdb/pull/47).



### Reporting your use case



If you maintain a public platform/tool using sysreqsdb, make a PR to this repo updating the [section below](#use-cases-of-the-database). Please put your tool at the very end of the list.



## Use cases of the database



* [R-hub](https://builder.r-hub.io/)



* The [`codemetar` package](https://github.com/ropensci/codemetar), R package for the [CodeMeta project](https://codemeta.github.io/), uses the sysreqs API to parse the SystemRequirements field.



* The [`containerit` package](https://github.com/o2r-project/containerit) uses the sysreqs API to derive system requirements of packages for automatically creating a Dockerfile based on a collection of packages.



## License



MIT © The R Consortium