guix.install {guix.install}

guix.install

Description

This procedure installs a given package with Guix. If the package is available in any enabled Guix channel, the package and its dependencies will be installed from there.

If the package is not available in Guix the procedure attempts to generate a package definition by recursively importing metadata from CRAN, Bioconductor, or a git/mercurial repository. Upon successful generation of package definitions in ~/.Rguix/packages.scm the package is installed with Guix.

The file ~/.Rguix/packages.scm is only appended to for reproducibility reasons. Each entry has a comment with a timestamp for convenience. The package definitions in that file could be upstreamed to a Guix channel to make it easier for others to reproduce the environment. Consider sending package definitions to either the Guix project or the Guix Science project.

Usage

guix.install(package, profile = NULL, guix = "guix", archive = NULL,
  cacheFile = NULL, stdout = "", stderr = "")

Arguments

package

The name of the R package to be installed as used on CRAN or Bioconductor, or a HTTP URL of a git repository holding an R package.

profile

The target Guix profile where the package should be installed. By default this is the default Guix profile at $HOME/.guix-profile.

guix

The absolute file name of the guix executable. By default this is just guix and will be searched on the user's PATH.

archive

This argument is used to override the Guix importer's archive option, e.g. to explicitly specify that the package should be imported from Bioconductor or from a Mercurial repository.

cacheFile

The absolute file name of the file where the imported package definitions should be recorded. When NULL this is $HOME/.Rguix/packages.scm.

stdout

Use this argument to redirect or silence Guix output printed to the standard output stream. The default value is "", causing all Guix messages to be printed to the console.

stderr

Use this argument to redirect or silence Guix output printed to the standard error stream. The default value is "", causing all Guix errors to be printed to the console.

Value

This procedure is run for its side-effects.

Author(s)

Ricardo Wurmus, [e-mail]

Examples

## Not run: 
guix.install("methylKit", cacheFile=tempfile())
guix.install("methylKit", profile="/home/foo/custom/.guix-profile", cacheFile=tempfile())
guix.install("methylKit", guix="/gnu/remote/bin/guix", cacheFile=tempfile())

## End(Not run)