diff options
-rw-r--r-- | .Rbuildignore | 1 | ||||
-rw-r--r-- | DESCRIPTION | 21 | ||||
-rw-r--r-- | NAMESPACE | 1 | ||||
-rw-r--r-- | man/guix.install-package.Rd | 40 | ||||
-rw-r--r-- | man/guix.install.Rd | 65 |
5 files changed, 128 insertions, 0 deletions
diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..a40c534 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1 @@ +^manifest.scm
\ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..f6e1bb2 --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,21 @@ +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 new file mode 100644 index 0000000..30ebb35 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1 @@ +export("guix.install") diff --git a/man/guix.install-package.Rd b/man/guix.install-package.Rd new file mode 100644 index 0000000..9abf4de --- /dev/null +++ b/man/guix.install-package.Rd @@ -0,0 +1,40 @@ +\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 --- /dev/null +++ b/man/guix.install.Rd @@ -0,0 +1,65 @@ +\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 } |