@sjcrh/proteinpaint-r v2.129.6

Installation

Docker

This is already included in the deps image and other images that use it as a base image.

Mac

Go to the Downloads directory

cd ~/Downloads

Download the R .pkg file, where VERSION is the same version of R specified in Dockerfile (see proteinpaint/container/deps/Dockerfile)

arm64-based (Apple silicon):

curl -O https://cran.r-project.org/bin/macosx/big-sur-arm64/base/R-{VERSION}-arm64.pkg

Intel-based:

curl -O https://cran.r-project.org/bin/macosx/big-sur-x86_64/base/R-{VERSION}-x86_64.pkg

Open the .pkg file and follow the installation instructions.

Verify that the correct version of R was installed

R --version

Install R packages

Rscript ~/dev/sjpp/proteinpaint/R/utils/install.pkgs.R

New R dependencies

To add an R package as a new dependency:

• For a CRAN package, add it to "utils/cran.pkgs.txt"
• For a Bioconductor package, add it to "utils/bioconductor.pkgs.txt"

Then re-build the deps image, as described here: https://github.com/stjude/proteinpaint/wiki/Buiding-a-deps-image