Install R dependencies inside a throwaway Docker container

The Docker-backed twin of repro_install_deps(): same return contract, same throwaway-library semantics, but the actual install.packages()/ remotes::install_github() call runs INSIDE a container (default networking, since CRAN/GitHub must be reachable), writing into lib_dir via a bind mount — so the run phase (repro_run_scripts_docker()), which mounts the same lib_dir with the network off, finds the packages already there.

Usage

repro_install_deps_docker(
  install_deps,
  lib_dir,
  image = "rocker/r-ver:latest",
  timeout = 600
)

Arguments

install_deps

a data frame as produced inside reproducibility_check() (package, source, ref, base) — the non-base rows of repro_dependencies()'s output

lib_dir

throwaway library directory ON THE HOST (created if absent); bind-mounted into the container at /rlib

image

the Docker image to install into (see .repro_docker_image_for())

timeout

per-package-batch timeout in seconds for the whole install container run (default 600 — installs can be slow, esp. compiling from source)

Value

a data frame with package, source, installed (logical), message (error text on failure, else ""), via_archive (TRUE when the package was not on CRAN and came from the CRAN Archive; a package not on CRAN is first looked for on Bioconductor, see .repro_docker_elsewhere_lines()), category (see .repro_classify_install_message(); NA for a successful install), version_recorded, version_installed and version_note — same columns as repro_install_deps() so callers do not need to branch on which backend ran. A row with a version is treated as there (see repro_install_deps()).

Details

Unlike repro_install_deps(), there is no cran_to_main_lib option: a container has no access to (and must not be given access to) the host's real R library, so every install always goes into the throwaway lib_dir.

Examples

if (FALSE) { # \dontrun{
# needs Docker
deps <- repro_dependencies("library(pwr)")
repro_install_deps_docker(deps, file.path(tempdir(), "lib"))
} # }