Add minimal R package files and directories.

5 files changed, 128 insertions, 0 deletions

diff --git a/.Rbuildignore b/.Rbuildignore
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+^manifest.scm
\ No newline at end of file
diff --git a/DESCRIPTION b/DESCRIPTION
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+Package: guix.install
+Type: Package
+Title: Install R Packages with GNU Guix
+Version: 1.0.0
+Date: 2022-04-06
+Author: Ricardo Wurmus
+Maintainer: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
+Description: This R package provides a single procedure guix.install,
+  which allows R users to install R packages via Guix right from within
+  their running R session.  If the requested R package does not exist
+  in Guix at this time, the package and all its missing dependencies
+  will be imported recursively and the generated package definitions
+  will be written to ~/.Rguix/packages.scm.  This record of imported
+  packages can be used later to reproduce the environment, and to add
+  the packages in question to a proper Guix channel (or Guix itself).
+  guix.install not only supports installing packages from CRAN, but
+  also from Bioconductor or even arbitrary git or mercurial
+  repositories, replacing the need for installation via devtools.
+Depends: R (>= 3.6.0)
+Imports: RUnit
+License: GPL (>= 3)
\ No newline at end of file
diff --git a/NAMESPACE b/NAMESPACE
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+export("guix.install")
diff --git a/man/guix.install-package.Rd b/man/guix.install-package.Rd
new file mode 100644
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+\name{guix.install-package}
+\alias{guix.install-package}
+\encoding{UTF-8}
+\docType{package}
+\title{guix.install: Install R Packages Reproducibly with Guix}
+\description{
+\packageDescription{guix.install}
+}
+\details{
+
+\packageIndices{guix.install}
+
+This package lets you install any R package through Guix from within a
+running R session.  If a desired R package is not yet available in any
+of your Guix channels, this package will leverage the recursive package
+importing facilities that Guix provides and transparently import
+packages from CRAN, Bioconductor, or any Mercurial or Git repository
+before installing them with Guix.
+
+This replaces the need for installers like devtools and exposes
+reproducible package management features through a familiar interface
+within R.
+}
+\author{
+\packageAuthor{guix.install}
+
+Maintainer: \packageMaintainer{guix.install}
+}
+\references{
+Courtès L., Wurmus R. (2015) Reproducible and User-Controlled Software Environments in HPC with Guix. In: Hunold S. et al. (eds) Euro-Par 2015: Parallel Processing Workshops. Euro-Par 2015. Lecture Notes in Computer Science, vol 9523. Springer, Cham. \doi{10.1007/978-3-319-27308-2_47}
+}
+\keyword{ package }
+\keyword{ utilities }
+\examples{
+\dontrun{
+guix.install("methylKit")
+guix.install("methylKit", profile="/home/foo/custom/.guix-profile")
+guix.install("methylKit", guix="/gnu/remote/bin/guix")
+}
+}
diff --git a/man/guix.install.Rd b/man/guix.install.Rd
new file mode 100644
index 0000000..b071377
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+++ b/man/guix.install.Rd
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+\name{guix.install}
+\alias{guix.install}
+\encoding{UTF-8}
+\title{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 \code{~/.Rguix/packages.scm} the
+  package is installed with Guix.
+
+  The file \code{~/.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
+  \href{https://guix.gnu.org/en/contribute/}{Guix project} or the
+  \href{https://github.com/guix-science/guix-science}{Guix Science project}.
+}
+\usage{
+guix.install(package, profile = NULL, guix = "guix", archive = NULL)
+}
+\arguments{
+  \item{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.
+  }
+  \item{profile}{
+    The target Guix profile where the package should be installed.  By
+    default this is the default Guix profile at
+    \code{$HOME/.guix-profile}.
+  }
+  \item{guix}{
+    The absolute file name of the \code{guix} executable.  By default
+    this is just \code{guix} and will be searched on the user's \code{PATH}. 
+  }
+  \item{archive}{
+    This argument is used to override the Guix importer's \code{archive}
+    option, e.g. to explicitly specify that the package should be imported
+    from Bioconductor or from a Mercurial repository.
+  }
+}
+\value{
+  This procedure is run for its side-effects.
+}
+\author{
+  Ricardo Wurmus, \email{ricardo.wurmus@mdc-berlin.de}
+}
+
+\examples{
+\dontrun{
+guix.install("methylKit")
+guix.install("methylKit", profile="/home/foo/custom/.guix-profile")
+guix.install("methylKit", guix="/gnu/remote/bin/guix")
+}
+}
+
+\keyword{ utilities }
+\concept{ package management }
+\concept{ reproducibility }