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rOpenSci - open tools for open science

rOpenSci - open tools for open science
Open Tools and R Packages for Open Science
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Published
Author Jeroen Ooms

What is renv RStudio’s renv package is a powerful dependency management toolkit for R. It allows you to create a lockfile that records the exact versions of R packages used in a given project, and provides tooling to install exactly those same versions on another machine, or at a later point in time. This is very useful to create an isolated project environment for reproducibility or production purposes.

Published
Author Jeroen Ooms

Continuous deployment in r-universe A major difference between r-universe and static repositories like CRAN and BioConductor is continuous deployment: packages in r-universe are continuously built in CI and immediately deployed to our package server. This package server stores binaries and metadata in a database, which enables us to dynamically query and expose all the package data through APIs, dashboards, feeds, etc.

Published
Authors Jeroen Ooms, Maëlle Salmon

Have you ever found a command-line tool that’s perfect for getting your job done, and wanted to use it from an R script or package?E.g. some sort of scientific software providing a specific functionality made available though a command-line interface (CLI)? In this post, we have a look at a few options for writing such CLI wrappers in R.In particular, we compare the base R functions system() and system2(), the sys package and the processx

Published
Author Jeroen Ooms

TLDR: As of today, the pkgdown sites for all rOpenSci packages on our docs server are built on r-universe. This is an internal change; no action is required for package maintainers.From Jenkins to r-universe For the past 2 years we have been using a Jenkins server to automatically build the pkgdown sites for all rOpenSci packages, which get published on https://docs.ropensci.org.

Published
Author Jeroen Ooms

Browsing articles on R-universe In the past weeks we have extended the R-universe build system and front-ends with some new features for publishing articles . Articles can be used for documentation of R packages, but also for other purposes, such as reports, tutorials, papers, or research compendia.Publishing of articles in R-universe is based on the R vignette system, and we may add support for other types of articles later on. The

Published
Author Jeroen Ooms

The R-universe build system The R-universe system is a complex effort, consisting of numerous frontend and backend pieces that operate across various platforms. A key challenge in developing such a system is managing overall complexity by finding ways to reduce the problem into smaller, loosely coupled components, which can be thought of, and developed, somewhat independently.