repositories

A list of CRAN=like repositories to fetch packages from. Packages will be installed from the first repository a resolvable version is found in, thus the order matters!! For more information, refer to the Resolution section. By default, packages are fetched as binaries when possible.

Options

• alias - Used for self-organization and to specify a certain repository source for a dependency
• url - The URL to the CRAN-like repository from which to fetch packages
• force_source optional - Force all packages coming from the repository to be source

  Default: false

Tip

To improve reproducibility across systems, linux binaries are fetched using the pattern set by Posit Package Manager. Therefore, it is recommended to not include the additional linux path elements required in base R.

Example

repositories = [
    { alias = "PPM", url = "https://packagemanager.posit.co/cran/latest" },
    { alias = "BioCsoft", url = "https://bioconductor.org/packages/3.21/bioc", force_source = true },
]

Other Repositories

Currently, rv is tuned to best support CRAN and PPM style repositories, but there are a few specific repositories to call out:

Bioconductor

Bioconductor is just a collection of CRAN-like repositories. In R itself, tools like BiocManager expands the repositories and sets them, so that when you call install.packages() it will search through them to find the package of interest.

While it is likely, we will include a configuration to handle the repository expansion internally, the onus remains on the user.

Below is an example expansion, where the bioconductor version and which repositories to include can vary based on the R version and packages of interest:

repositories = [
    { alias = "BioCsoft", url = "https://bioconductor.org/packages/3.21/bioc" },
    { alias = "BioCann", url = "https://bioconductor.org/packages/3.21/data/annotation" },
    { alias = "BioCexp", url = "https://bioconductor.org/packages/3.21/data/experiment" },
    { alias = "BioCworkflows", url = "https://bioconductor.org/packages/3.21/workflows" },
]

R-Universe

R-Universe is formatted like a CRAN-like repository, but is missing a critical component: there is no archive. Since reproducibility is at the forefront of design considerations with rv, we currently consider packages sourced from R-universe as git dependencies from the beginning. While this may lead to a temporary slow down due to compilation, it is more reproducible. We may consider downloading compiled binaries for available packages in the future if the need arises.