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.
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 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(...))