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Create a package reference

Source: R/pkg_ref_class.R
pkg_ref.Rd

Create a package reference from package name or filepath, producing an object in which package metadata will be collected as risk assessments are performed. Depending on where the package was found - whether it is found as source code, in a local library or from a remote host - an S3 subclass is given to allow for source-specific collection of metadata. See 'Details' for a breakdown of subclasses. Different sources can be specified by passing a subclass as an arguemnt named 'source', see details.

Usage

pkg_ref(x, ...)

pkg_install(x, lib.loc = NULL)

pkg_source(x)

pkg_cran(x, repos = getOption("repos", "https://cran.rstudio.com"))

pkg_bioc(x)

pkg_missing(x)

pkg_library(lib.loc)

as_pkg_ref(x, ...)

Arguments

x

A singular character value, character vector or list of character values of package names or source code directory paths.

...

Additional arguments passed to methods.

lib.loc

The path to the R library directory of the installed package.

repos

URL of CRAN repository to pull package metadata.

Value

When a single value is provided, a single pkg_ref object is returned, possibly with a subclass based on where the package was found. If a vector or list is provided, a list_of_pkg_ref object constructed with list_of is returned, which can be considered analogous to a list. See 'Details' for further information about pkg_ref subclasses.

Details

Package reference objects are used to collect metadata pertaining to a given package. As data is needed for assessing a package's risk, this metadata populates fields within the package reference object.

The pkg_ref S3 subclasses are used extensively for divergent metadata collection behaviors dependent on where the package was discovered. Because of this, there is a rich hierarchy of subclasses to articulate the different ways package information can be found.

A source argument can be passed using the `source` argument. This will override the logic that riskmetric does when determining a package source. This can be useful when you are scoring the most recent version present on a repository, or testing a specific library.

  • pkg_ref A default class for general metadata collection.

    • pkg_source A reference to a source code directory.

    • pkg_install A reference to a package installation location in a package library. A specific library can be passed by passing the path to the library as the parameter `lib.loc`

    • pkg_remote A reference to package metadata on a remote server.

      • pkg_cran_remote A reference to package information pulled from the CRAN repository.

      • pkg_bioc_remote A reference to package information pulled from the Bioconductor repository.

      • pkg_git_remote A reference to a package source code git repository. (not yet implemented)

Package Cohorts

*Experimental!* Package cohorts are structures to determine the risk of a set of packages. `pkg_library()` can be called to create a object containing the pkg_ref objects of all packages in a system library.

Examples

if (FALSE) { # \dontrun{
# riskmetric will check for installed packages by default
ref_1 <- pkg_ref("utils")
ref_1$source # returns 'pkg_install'

# lib.loc can be used to specify a library for pkg_install
ref_3 <- pkg_ref("utils", source = "pkg_install", lib.loc = .libPaths()[1])

# You can also override this behavior with a source argument
ref_2 <- pkg_ref("utils", source = "pkg_cran_remote")
ref_2$source  # returns 'pkg_cran_remote'
} # }