Using renv with Bioconductor

renv has been designed to work together as seamlessly as possible with the Bioconductor project. This vignette outlines some of the extra steps that may be required when using renv with packages obtained from Bioconductor.

Initializing a Project

To initialize renv in a project using Bioconductor, you can pass the bioconductor argument to renv::init():

# use the latest-available Bioconductor release
renv::init(bioconductor = TRUE)

# use a specific version of Bioconductor
renv::init(bioconductor = "3.14")

This will tell renv to activate the appropriate Bioconductor repositories, and to use those repositories when attempting to restore packages.

Bioconductor Releases

Bioconductor prepares different versions of its package repositories, for use with different versions of R. The version of Bioconductor used within a particular renv project is stored both as a project setting, and also within the project lockfile. This allows you to “lock” a particular project to a particular Bioconductor release, even as new Bioconductor releases are made available for newer versions of R.

To set the version of Bioconductor used in a project, you can use:

renv::settings$bioconductor.version("3.14")

If you later choose to upgrade R, you may need to upgrade the version of Bioconductor used as well.

If you want to override the Bioconductor repositories used by renv, you can also explicitly set the following option:

options(renv.bioconductor.repos = c(...))