Skip to content

UPDATE-R.md

Latest commit

 

History

History
124 lines (89 loc) · 3.25 KB

UPDATE-R.md

File metadata and controls

124 lines (89 loc) · 3.25 KB

Updating R Package Dependencies

The pinned R dependencies are managed via renv. renv.lock records the exact version of every package (direct and transitive).

To update it, spin up an ephemeral container from the same base image used by the Dockerfile, mount this repository into it, and run the renv commands there. The only file that needs to be committed afterwards is the updated renv.lock.

Procedure

1. Build a local helper image with R and build dependencies

Run this once from the root of the repository (re-run whenever the base image SHA in the FROM line of the Dockerfile changes):

docker build -t gdal-r-update - <<'EOF'
FROM ghcr.io/osgeo/gdal:ubuntu-small-3.11.3
RUN DEBIAN_FRONTEND=noninteractive apt-get update -qq && \
    apt-get install -y --no-install-recommends \
      build-essential \
      curl            \
      r-base          \
      r-cran-renv     \
      gfortran        \
      libblas-dev     \
      liblapack-dev   \
      libuv1-dev      \
      pandoc          \
      zlib1g-dev
EOF

This installs R and all build dependencies as root inside a throwaway image.

2. Launch an interactive container

docker run --rm -it \
  -v "$(pwd)":/work \
  -u "$(id -u):$(id -g)" \
  -e HOME=/tmp \
  gdal-r-update \
  bash

Running as your own UID/GID (-u) ensures that any files written to the mounted repository — including the updated renv.lock — are owned by you. -e HOME=/tmp gives renv a writable home directory inside the container.

3. Restore the current state

cd /work
export RENV_PATHS_LIBRARY=/tmp/renv-lib   # keep packages out of the mounted volume
Rscript -e 'renv::restore()'

This installs all packages at the versions currently recorded in renv.lock. It is required before updating so that renv knows what is installed.

Use Rscript -e 'options(Ncpus = parallel::detectCores()); renv::restore() to get some speedup by building the individual packages in parallel.

4. Update packages

Update all packages to the latest CRAN versions:

Rscript -e 'renv::update()'

Update a single package:

Rscript -e 'renv::update("echarts4r")'

Install a new package and add it to the lockfile:

Rscript -e 'install.packages("newpkg")'

5. Write the new versions to the lockfile

Rscript -e 'renv::snapshot()'

This overwrites renv.lock with the currently installed versions. Because /work is a bind mount, the file is updated directly on your host.

6. Commit

git add renv.lock
git commit -m "renv: update R package dependencies"

Notes

  • The directly required packages are: rmarkdown, echarts4r, snow, snowfall, getopt. All other entries in renv.lock are their transitive dependencies.
  • snapshot.type is set to "all" in renv/settings.json, so every installed package (including indirect dependencies) is captured in the lockfile.
  • renv/library/ is listed in renv/.gitignore and must not be committed.
  • The R.Version field in renv.lock reflects the R version inside the container. Make sure the base image SHA in the docker run command matches the one in the FROM line of the Dockerfile to keep R versions consistent.