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223 changes: 223 additions & 0 deletions content/post/2024-03-21-containers/index.Rmd
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---
slug: rhub-containers
title: "Docker containers for R users and developers"
authors:
- Gábor Csárdi
date: "2024-03-21"
tags:
- Docker
- containers
- R versions
output: hugodown::hugo_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(fig.path = "", comment = "")
# knitr hook to make images output use Hugo options
knitr::knit_hooks$set(
plot = function(x, options) {
hugoopts <- options$hugoopts
paste0(
"{{<figure src=",
'"', x, '" ',
if (!is.null(hugoopts)) {
glue::glue_collapse(
glue::glue('{names(hugoopts)}="{hugoopts}"'),
sep = " "
)
},
">}}\n"
)
}
)
```

```{r, include = FALSE, cache = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
out.width = "100%",
asciicast_theme = "pkgdown"
)
```

## TL;DR

If you need a Docker container with R, or need to run a specific R version
or need to run R on a specific platform, then chances are, you don't need
to compile R or build your own Docker image. Take a look at the links
below.

## [`rstudio/r-docker`](https://github.com/rstudio/r-docker)

Containers corresponding to Posit's R builds from
[rstudio/r-builds](https://github.com/rstudio/r-builds)

Advantages:

* Many Linux distributions, currently all supported versions of Ubuntu,
Debian, CentOS, Rocky Linux, and OpenSUSE.
* Extensively tested. These Ubuntu (20.04 currently) builds are used on
[Posit Cloud](https://posit.cloud/),
[shinyapps.io](https://shinyapps.io/), and the
[`r-lib/actions/setup-r`](https://github.com/r-lib/actions/tree/v2-branch/setup-r)
GitHub Action also installs these on Linux.
* They support all versions of R from R 3.1.0, and R-devel.
* It is possible to install multiple versions of R on these containers.

List of Docker images at the time of writing:

Tag | Description
----------------------------------+-----------------------------------------------------------
`rstudio/r-base:<x.y.z>-<distro>` | R version `x.y.z` on the specified OS
`rstudio/r-base:<x.y>-<distro>` | Latest R version in the `x.y` branch, on the specified OS

`<x.y.z>` can be any version from `3.1.0` to `4.3.3` or `devel`.
`<x.y>` can be any minor version from `3.1` to `4.3`.

`<distro>` can be one of `focal`, `jammy`, `bullseye`, `bookworm`,
`centos7`, `rockylinux8` `rockylinux9`, `opensuse154` and `opensuse155`.

See the [GitHub repo](https://github.com/rstudio/r-docker#releases-and-tags)
or [Docker Hub](https://hub.docker.com/r/rstudio/r-base/tags?page=1&name=4.3.3)
for the current list of containers.

## [`r-lib/rig`](https://github.com/r-lib/rig#id-container)

Some of these containers use the same R builds as `rstudio/r-docker`.

Advantages:

* Many Linux Distributions, currently all supported versions of Ubuntu,
Debian, Fedora and OpenSUSE.
* Extensively tested. These Ubuntu (20.04 `linux/amd64` currently) builds
are used on [Posit Cloud](https://posit.cloud/),
[shinyapps.io](https://shinyapps.io/), and the
[`r-lib/actions/setup-r`](https://github.com/r-lib/actions/tree/v2-branch/setup-r)
GitHub Action also installs these on Linux.
* They come with [rig](https://github.com/r-lib/rig), to be able to add
more R versions easily.
* They come with [pak](https://github.com/r-lib/pak), to be able to install
R packages easily, including automatic system dependency
installation.
* They are available for `linux/amd64` and `linux/arm64` architectures.
* The `linux/amd64` Ubuntu, Debian and OpenSUSE containers are set up to
use Posit Public Package Manager to install binary builds of R packages.
* The `ghcr.io/r-lib/rig/multi` container comes with the latest versions
of the six last R minor branches, including R-next and R-devel,
preinstalled.

List of Docker images at the time of writing:

Tag | Description
-------------------------------------+----------------------------------
`ghcr.io/r-lib/rig/multi` | Last 6 minor R versions
`ghcr.io/r-lib/rig/<distro>-release` | R-release on the specified distro
`ghcr.io/r-lib/rig/<distro>-devel` | R-devel on the specified distro

`<distro>` can be one of `ubuntu-22.04`, `ubuntu-20.04`, `debian-12`,
`debian-11`, `debian-10`, `fedora-39`, `fedora-38`, `opensuse-15.5`,
`opensuse-15.4`.

See the current list of containers at the
[GitHub repository](https://github.com/r-lib/rig#all-containers).

## [`r-hub/r-minimal`](https://github.com/r-hub/r-minimal)

Minimal containers on Alpine Linux. These containers have a very minimal
R installation, and they are aimed for cloud deployments and serverless
apps.

Advantages:

* Very small image size. The current R 4.3.3 `linux/amd64` container is
20.8 MB compressed and 35.7 MB uncompressed.
* They are available for `linux/amd64` and `linux/arm64` architectures.
* They support the last four minor R releases, and R-next and R-devel.
* They come with tools to help with package and system dependency
installation and cleanup.

List of images at the time of writing

Tag | Description
------------------------------------------+----------------------------------------
`ghcr.io/r-hub/r-minimal/r-minimal:devel` | R-devel
`ghcr.io/r-hub/r-minimal/r-minimal:next` | Next version of R, typically R-patched
`ghcr.io/r-hub/r-minimal/r-minimal:x.y.z` | R `x.y.z`
`ghcr.io/r-hub/r-minimal/r-minimal:x.y` | Last release of the `x.y` branch

See the current list of containers at the
[GitHub repository](https://github.com/r-hub/r-minimal#supported-r-versions).

## [`r-hub/containers`](https://github.com/r-hub/containers)

Many of them are set up similarly to the Linux systems CRAN uses for
[regular](https://cran.r-project.org/web/checks/check_flavors.html) and
[extra](https://cran.r-project.org/web/checks/check_issue_kinds.html)
package checks.

Advantages:

* They are built daily, with the most recent R-devel.
* They come with [pak](https://github.com/r-lib/pak), to be able to install
R packages easily, including automatic system dependency
installation.
* Most containers are set up to use package binaries from
[`r-hub/repos`](https://github.com/r-hub/repos).

List of containers at the time of writing:

Tag | Description
--------------------------------------+----------------------------------------------------
`ghcr.io/r-hub/containers/atlas` | Tests with alternative BLAS/LAPACK implementations
`ghcr.io/r-hub/containers/centos7` | Last 5 minor releases, R-next, R-devel on CentOS 7
`ghcr.io/r-hub/containers/clang-asan` | Tests of memory access errors using AddressSanitizer or Undefined Behavior Sanitizer
`ghcr.io/r-hub/containers/clang16` | Checks with Clang 16.x.y
`ghcr.io/r-hub/containers/clang17` | Checks with Clang 17.x.y
`ghcr.io/r-hub/containers/clang18` | Checks with Clang 18.x.y
`ghcr.io/r-hub/containers/donttest` | Tests including `\donttest` examples
`ghcr.io/r-hub/containers/gcc13` | Checks with GCC 13.x
`ghcr.io/r-hub/containers/intel` | Checks with Intel oneAPI 2023.x compilers
`ghcr.io/r-hub/containers/mkl` | Tests with alternative BLAS/LAPACK implementations
`ghcr.io/r-hub/containers/nold` | Tests without long double
`ghcr.io/r-hub/containers/nosuggests` | Tests without suggested packages
`ghcr.io/r-hub/containers/valgrind` | Tests of memory access errors using valgrind


See the [current list of containers](https://r-hub.github.io/containers/).

## [r-hub/evercran`](https://github.com/r-hub/evercran)

Includes containers for all R versions ever released, including very old
and very-very old versions.

Advantages:

* Supports all R versions, starting from R 0.0 (alpha-test) to the latest
release.
* Every container is set up to use an appropriate daily snapshot of CRAN.
* Older R versions use a similarly old Debian distro, so system
dependencies work better.
* Newer R versions are available for `linux/amd64` and `linux/arm64`
platforms. (Containers before R 3.0.0 use `linux/i386`.)

List of containers at the time of writing:

Tag | Description
----------------------------------+-----------------------------------
`ghcr.io/r-hub/evercran/<x.y.z>` | Container with R `x.y.z`
`ghcr.io/r-hub/evercran/pre` | All R versions from 0.0 to 0.16.1
`ghcr.io/r-hub/evercran/0.x` | R 0.49 – R 1.0.0
`ghcr.io/r-hub/evercran/1.x` | R 1.0.0 – R 1.9.1
`ghcr.io/r-hub/evercran/2.x` | R 2.0.0 – R 2.15.3

`<x.y.z>` can be any released R version from `0.0` to the latest release
(currently `4.3.3`).

See the current list of containers on the
[GitHub page](https://github.com/r-hub/evercran#containers-with-multiple-r-versions).

## Links

* [The Rocker Project](https://rocker-project.org/): Docker Containers for
the R Environment
150 changes: 150 additions & 0 deletions content/post/2024-03-21-containers/index.md
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---
slug: rhub-containers
title: "Docker containers for R users and developers"
authors:
- Gábor Csárdi
date: "2024-03-21"
tags:
- Docker
- containers
- R versions
output: hugodown::hugo_document
rmd_hash: e98dcd1279f66d9e

---

## TL;DR

If you need a Docker container with R, or need to run a specific R version or need to run R on a specific platform, then chances are, you don't need to compile R or build your own Docker image. Take a look at the links below.

## [`rstudio/r-docker`](https://github.com/rstudio/r-docker)

Containers corresponding to Posit's R builds from [rstudio/r-builds](https://github.com/rstudio/r-builds)

Advantages:

- Many Linux distributions, currently all supported versions of Ubuntu, Debian, CentOS, Rocky Linux, and OpenSUSE.
- Extensively tested. These Ubuntu (20.04 currently) builds are used on [Posit Cloud](https://posit.cloud/), [shinyapps.io](https://shinyapps.io/), and the [`r-lib/actions/setup-r`](https://github.com/r-lib/actions/tree/v2-branch/setup-r) GitHub Action also installs these on Linux.
- They support all versions of R from R 3.1.0, and R-devel.
- It is possible to install multiple versions of R on these containers.

List of Docker images at the time of writing:

| Tag | Description |
|---------------------------|---------------------------------------------|
| `rstudio/r-base:<x.y.z>-<distro>` | R version `x.y.z` on the specified OS |
| `rstudio/r-base:<x.y>-<distro>` | Latest R version in the `x.y` branch, on the specified OS |

`<x.y.z>` can be any version from `3.1.0` to `4.3.3` or `devel`. `<x.y>` can be any minor version from `3.1` to `4.3`.

`<distro>` can be one of `focal`, `jammy`, `bullseye`, `bookworm`, `centos7`, `rockylinux8` `rockylinux9`, `opensuse154` and `opensuse155`.

See the [GitHub repo](https://github.com/rstudio/r-docker#releases-and-tags) or [Docker Hub](https://hub.docker.com/r/rstudio/r-base/tags?page=1&name=4.3.3) for the current list of containers.

## [`r-lib/rig`](https://github.com/r-lib/rig#id-container)

Some of these containers use the same R builds as `rstudio/r-docker`.

Advantages:

- Many Linux Distributions, currently all supported versions of Ubuntu, Debian, Fedora and OpenSUSE.
- Extensively tested. These Ubuntu (20.04 `linux/amd64` currently) builds are used on [Posit Cloud](https://posit.cloud/), [shinyapps.io](https://shinyapps.io/), and the [`r-lib/actions/setup-r`](https://github.com/r-lib/actions/tree/v2-branch/setup-r) GitHub Action also installs these on Linux.
- They come with [rig](https://github.com/r-lib/rig), to be able to add more R versions easily.
- They come with [pak](https://github.com/r-lib/pak), to be able to install R packages easily, including automatic system dependency installation.
- They are available for `linux/amd64` and `linux/arm64` architectures.
- The `linux/amd64` Ubuntu, Debian and OpenSUSE containers are set up to use Posit Public Package Manager to install binary builds of R packages.
- The `ghcr.io/r-lib/rig/multi` container comes with the latest versions of the six last R minor branches, including R-next and R-devel, preinstalled.

List of Docker images at the time of writing:

| Tag | Description |
|--------------------------------------|-----------------------------------|
| `ghcr.io/r-lib/rig/multi` | Last 6 minor R versions |
| `ghcr.io/r-lib/rig/<distro>-release` | R-release on the specified distro |
| `ghcr.io/r-lib/rig/<distro>-devel` | R-devel on the specified distro |

`<distro>` can be one of `ubuntu-22.04`, `ubuntu-20.04`, `debian-12`, `debian-11`, `debian-10`, `fedora-39`, `fedora-38`, `opensuse-15.5`, `opensuse-15.4`.

See the current list of containers at the [GitHub repository](https://github.com/r-lib/rig#all-containers).

## [`r-hub/r-minimal`](https://github.com/r-hub/r-minimal)

Minimal containers on Alpine Linux. These containers have a very minimal R installation, and they are aimed for cloud deployments and serverless apps.

Advantages:

- Very small image size. The current R 4.3.3 `linux/amd64` container is 20.8 MB compressed and 35.7 MB uncompressed.
- They are available for `linux/amd64` and `linux/arm64` architectures.
- They support the last four minor R releases, and R-next and R-devel.
- They come with tools to help with package and system dependency installation and cleanup.

List of images at the time of writing

| Tag | Description |
|-------------------------------------|-----------------------------------|
| `ghcr.io/r-hub/r-minimal/r-minimal:devel` | R-devel |
| `ghcr.io/r-hub/r-minimal/r-minimal:next` | Next version of R, typically R-patched |
| `ghcr.io/r-hub/r-minimal/r-minimal:x.y.z` | R `x.y.z` |
| `ghcr.io/r-hub/r-minimal/r-minimal:x.y` | Last release of the `x.y` branch |

See the current list of containers at the [GitHub repository](https://github.com/r-hub/r-minimal#supported-r-versions).

## [`r-hub/containers`](https://github.com/r-hub/containers)

Many of them are set up similarly to the Linux systems CRAN uses for [regular](https://cran.r-project.org/web/checks/check_flavors.html) and [extra](https://cran.r-project.org/web/checks/check_issue_kinds.html) package checks.

Advantages:

- They are built daily, with the most recent R-devel.
- They come with [pak](https://github.com/r-lib/pak), to be able to install R packages easily, including automatic system dependency installation.
- Most containers are set up to use package binaries from [`r-hub/repos`](https://github.com/r-hub/repos).

List of containers at the time of writing:

| Tag | Description |
|-------------------------------|-----------------------------------------|
| `ghcr.io/r-hub/containers/atlas` | Tests with alternative BLAS/LAPACK implementations |
| `ghcr.io/r-hub/containers/centos7` | Last 5 minor releases, R-next, R-devel on CentOS 7 |
| `ghcr.io/r-hub/containers/clang-asan` | Tests of memory access errors using AddressSanitizer or Undefined Behavior Sanitizer |
| `ghcr.io/r-hub/containers/clang16` | Checks with Clang 16.x.y |
| `ghcr.io/r-hub/containers/clang17` | Checks with Clang 17.x.y |
| `ghcr.io/r-hub/containers/clang18` | Checks with Clang 18.x.y |
| `ghcr.io/r-hub/containers/donttest` | Tests including `\donttest` examples |
| `ghcr.io/r-hub/containers/gcc13` | Checks with GCC 13.x |
| `ghcr.io/r-hub/containers/intel` | Checks with Intel oneAPI 2023.x compilers |
| `ghcr.io/r-hub/containers/mkl` | Tests with alternative BLAS/LAPACK implementations |
| `ghcr.io/r-hub/containers/nold` | Tests without long double |
| `ghcr.io/r-hub/containers/nosuggests` | Tests without suggested packages |
| `ghcr.io/r-hub/containers/valgrind` | Tests of memory access errors using valgrind |

See the [current list of containers](https://r-hub.github.io/containers/).

## [r-hub/evercran\`](https://github.com/r-hub/evercran)

Includes containers for all R versions ever released, including very old and very-very old versions.

Advantages:

- Supports all R versions, starting from R 0.0 (alpha-test) to the latest release.
- Every container is set up to use an appropriate daily snapshot of CRAN.
- Older R versions use a similarly old Debian distro, so system dependencies work better.
- Newer R versions are available for `linux/amd64` and `linux/arm64` platforms. (Containers before R 3.0.0 use `linux/i386`.)

List of containers at the time of writing:

| Tag | Description |
|----------------------------------|-----------------------------------|
| `ghcr.io/r-hub/evercran/<x.y.z>` | Container with R `x.y.z` |
| `ghcr.io/r-hub/evercran/pre` | All R versions from 0.0 to 0.16.1 |
| `ghcr.io/r-hub/evercran/0.x` | R 0.49 -- R 1.0.0 |
| `ghcr.io/r-hub/evercran/1.x` | R 1.0.0 -- R 1.9.1 |
| `ghcr.io/r-hub/evercran/2.x` | R 2.0.0 -- R 2.15.3 |

`<x.y.z>` can be any released R version from `0.0` to the latest release (currently `4.3.3`).

See the current list of containers on the [GitHub page](https://github.com/r-hub/evercran#containers-with-multiple-r-versions).

## Links

- [The Rocker Project](https://rocker-project.org/): Docker Containers for the R Environment