Run on your machine

Prerequisites

To run these containers on your machine you need:

  • Docker.
    • On Linux Docker is probably part of your distribution. Install the docker.io package on Debian and Ubuntu. See the Docker docs for other distributions.
    • On macOS, you can use Docker Desktop (free for non-commercial use), or install docker from Homebrew.
    • On Windows, you can use Docker Desktop (free for non-commercial use). It is possible to use Docker without Docker Desktop as well, but harder to set up.
  • A couple of gigabytes of disk space, depending on how many and which containers you run at the same time.

Run R CMD check on a tarball

  1. Create a directory, e.g. check. E.g. on Unix:

    mkdir check

  2. Put the source R package into this directory, e.g.

    R -q -e "download.packages('cli', 'check')"

  3. Start the container with the check directory mounted at /check and run the r-check command. E.g. for the gcc13 image you would run:

    docker run -v `pwd`/check:/check ghcr.io/r-hub/containers/gcc13:latest r-check

    If you are running this on a non-Intel machine (eg. an M1 mac), pass --platform=linux/amd64 to docker run. Note that this will make Docker emulate an x86_64 processor, which is usually 5-10 times slower than native execution.

  4. The result of the check will be in the check directory, in the usual <pkgname>.Rcheck directory.

Here is the complete output from a check of a very simple package, that has no dependencies, only some system dependencies:

mkdir check
R -q -e "download.packages('tiff', 'check')"
> download.packages('tiff', 'check')
trying URL 'https://cloud.r-project.org/src/contrib/tiff_0.1-11.tar.gz'
Content type 'application/x-gzip' length 68157 bytes (66 KB)
==================================================
downloaded 66 KB

     [,1]   [,2]
[1,] "tiff" "check/tiff_0.1-11.tar.gz"
docker run --platform=linux/amd64 -v `pwd`/check:/check \
  ghcr.io/r-hub/containers/gcc13:latest r-check
Checking /check/tiff_0.1-11.tar.gz
> pak::pkg_install('deps::/check/tiff_0.1-11.tar.gz', dependencies = TRUE)

→ Will download 1 package with unknown size.
ℹ No downloads are needed
ℹ Installing system requirements
ℹ Executing `sh -c dnf install -y libjpeg-turbo-devel libtiff-devel`
✔ :  [21.4s]

* using log directory ‘/check/tiff.Rcheck’
* using R Under development (unstable) (2023-01-23 r83671)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 13.0.1 20230117 (Red Hat 13.0.1-0)
    GNU Fortran (GCC) 13.0.1 20230117 (Red Hat 13.0.1-0)
* running under: Fedora Linux 38 (Container Image Prerelease)
* using session charset: UTF-8
* using options ‘--no-manual --no-build-vignettes’
* checking for file ‘tiff/DESCRIPTION’ ... OK
* this is package ‘tiff’ version ‘0.1-11’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for .dll and .exe files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘tiff’ can be installed ... WARNING
Found the following significant warnings:
  common.c:36:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/check/tiff.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 13.0.1 20230117 (Red Hat 13.0.1-0)’
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
  ‘-Werror=format-security’ ‘-Wp,-D_FORTIFY_SOURCE=2’
* checking compiled code ... OK
* checking examples ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/check/tiff.Rcheck/00check.log’
for details.
ls check/tiff.Rcheck/
00_pkg_src/ 00install.out   tiff-Ex.R   tiff-Ex.pdf
00check.log tiff/       tiff-Ex.Rout

Interactive debugging

This is similar to running R CMD check, but start bash instead of r-check, and use -ti to create an interactive session:

docker run -v `pwd`/check:/check ghcr.io/r-hub/containers/gcc13:latest bash

You’ll need to install the dependencies of the package. The easiest is to use pak, which is preinstalled in all containers. From the root directory of the extracted package call:

R -q -e "pak::pkg_install('deps::.', dependencies = TRUE)"

This installs all dependencies and system requirements of the package.

Multiple R versions

Some container images (e.g. centos7) have multiple versions of R installed. You can use rig ls to list all versions, and rig default <name> to set the default one. To run r-check with a certain R version, set the R_VERSION environment variable for the container. E.g.

docker run -ti --rm  --platform=linux/amd64 -v `pwd`/check:/check \
  -e "R_VERSION=3.6.3" ghcr.io/r-hub/containers/centos7:latest r-check