r-ver

1 Quick reference

2 Overview

rocker/r-ver is alternate image to r-base, with an emphasis on reproducibility.

Compared to r-base,

  • Builds on Ubuntu LTS rather than Debian and system libraries are tied to the Ubuntu version. Images will use the most recent LTS available at the time when the corresponding R version was released.
    • Since compatibility problems are likely to occur immediately after the release of a new Ubuntu LTS, the version to be used is the one that is at least 90 days past release.
      • rocker/r-ver:4.0.0 is based on Ubuntu 20.04 (ubuntu:focal) because no interval was set at the time of the Ubuntu 20.04 release.
  • Installs a fixed version of R itself from source, rather than whatever is already packaged for Ubuntu (the r-base stack gets the latest R version as a binary from Debian unstable).
  • The only platforms available are linux/amd64 and linux/arm64 (arm64 images are experimental and only available for rocker/r-ver 4.1.0 or later).
  • Set the Posit Public Package Manager (P3M, a.k.a RStudio Package Manager, RSPM) as default CRAN mirror. For the amd64 platform, RSPM serves compiled Linux binaries of R packages and greatly speeds up package installs.
  • Non-latest R version images installs all R packages from a fixed snapshot of CRAN mirror at a given date. This setting ensures that the same version of the R package is installed no matter when the installation is performed.
  • Provides images that are generally smaller than the r-base series.
Note

This document is for R 4.0.0 >= images. Please check the rocker-org/rocker-versioned repository for R <= 3.6.3 images.

3 Special tags

3.1 devel

The devel images are based on ubuntu:latest (the latest Ubuntu LTS version) and install the latest R-devel daily snapshot.

3.2 cuda

Tags which contain cuda (e.g. rocker/r-ver:4.0.0-cuda10.1) are alias of rocker/cuda.

Warning

cuda tags will be discontinued in the future, so please use rocker/cuda instead.

4 How to use

4.1 Switch the default CRAN mirror

As explained in the overview, rocker/r-ver may have set a past CRAN snapshot as the default repository. This is determined by the options set in the Rprofile. To use a different CRAN mirror, simply write a new setting in the Rprofile.

For example, the following Dockerfile sets the default repository to CRAN.

Dockerfile
FROM rocker/r-ver:4
RUN echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' >>"${R_HOME}/etc/Rprofile.site"
Tip

To do the same thing by a non-root user in a container, for example, the following command can be used.

Terminal
echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' | sudo sh -c 'cat - >>"${R_HOME}/etc/Rprofile.site"'
Tip

We can also use the script setup_R.sh included in rocker/r-ver.

Dockerfile
FROM rocker/r-ver:4
RUN /rocker_scripts/setup_R.sh https://packagemanager.posit.co/cran/__linux__/jammy/2023-01-29

The advantage of using this script is that if you specify a URL for binary installation from Posit Public Package Manager (P3M), it will rewrite the URL and switch to source installation on non-amd64 platforms.

For example, in the above example, https://packagemanager.posit.co/cran/__linux__/jammy/2023-01-29 is set for the amd64 platform, but https://packagemanager.posit.co/cran/2023-01-29 is set for the arm64 platform as the default CRAN mirror.

Or, if you want to temporarily change the CRAN mirror during an R session, use the options() function.

A common use case is when developing an R package and using the devtools::check() function; if the CRAN mirror is not changed from the default, an error like cannot open URL 'packagemanager.posit.co/cran/__linux__/jammy/latest/web/packages/packages.rds': HTTP status was '404 Not Found' may occur.

R Terminal
options(repos = c(CRAN = "https://cloud.r-project.org"))
devtools::check()

It is also possible to set up P3M and CRAN at the same time to achieve both binary installation and successful the devtools::check() function as follows. (rocker-org/rocker-versioned2#658)

Dockerfile
FROM rocker/r-ver:4
RUN echo 'options(repos = c(P3M = "https://packagemanager.posit.co/cran/__linux__/jammy/latest", CRAN = "https://cloud.r-project.org"))' >>"${R_HOME}/etc/Rprofile.site"

4.2 Selecting the BLAS implementation used by R

By default rocker/r-ver uses the OpenBLAS implementation for Linear Algebra1. But it is possible to switch for the reference BLAS implementation (as provided by the Debian package libblas-dev) using the Shared BLAS setup2.

Important

Calling Python numpy by the reticulate package on R using OpenBLAS may cause a segfault. This causes an error when trying to use Python packages like matplotlib or scikit-learn. (rocker-org/rocker-versioned2#471, numpy/numpy#21643)

If this error occurs, change the BLAS used by R to libblas as described below.

4.2.1 Checking which BLAS is in use

You can see the current BLAS configuration for R by using sessionInfo() function in R console.

R Terminal
sessionInfo()
#> R version 4.2.0 (2022-04-22)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.4 LTS
#>
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

Here for instance R uses OpenBLAS.

4.2.2 Switching BLAS implementations

You can switch BLAS used by R with the Debian update-alternatives script:

Terminal
ARCH=$(uname -m)
update-alternatives --set "libblas.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/blas/libblas.so.3"
update-alternatives --set "liblapack.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/lapack/liblapack.so.3"
Terminal
ARCH=$(uname -m)
update-alternatives --set "libblas.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/openblas-pthread/libblas.so.3"
update-alternatives --set "liblapack.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/openblas-pthread/liblapack.so.3"