R tools for the shell
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README.md

rt: R Tools for the Command Line

This package ships some command line utilities which simplify working with R packages from the command line. Many commands rt provides are just wrappers around devtools but ensure a valid exit code which is required to use these commands for shell scripting. Furthermore, rt allows you to maintain a collection of you favorite packages in a plain text file which you can add to your dotfiles and share across systems. This file may also contain git sources to keep you up to date with packages not yet released on CRAN.

Available Commands

  • rbuild to bundle a local package.
  • rcheck to check a local package.
  • rclean to remove .[o|so] files from a local package.
  • rclone to clone a GitHub package to your system
  • rcompile to compile Sweave (.Rnw) and Rmarkdown (.Rmd) files to HTML or PDF.
  • rcov to test the coverage of a local package.
  • rdoc to document a local package using roxygen.
  • rhub to upload a local package to rhub service.
  • rinstall to install a remote package, e.g. a package hosted on CRAN or GitHub.
  • rknit to knit a knitr document (.Rnw, .Rrst) to PDF.
  • rmake to make a local package (document and install).
  • rmarkdown to render a Rmarkdown (.Rmd) file.
  • rpkgdown to build static HTML documentation with pkgdown.
  • rrelease to release a local package to CRAN.
  • rremove to remove (uninstall) R packages.
  • rshine to run a shiny app.
  • rspell to check spelling in generated .Rd files.
  • rtest to test a local package.
  • rtstchk to test and check a local package.
  • rupdate to update all CRAN packages on your system, install missing CRAN packages listed in your collection ~/.rt/packages and update all packages with a git source.
  • rusage to check variable usage.
  • rvignette to build vignettes.
  • rwinbuild to upload a local package to the winbuilder service.

Call the respective command with --help to list available command line arguments. All commands are also available as regular R functions, using the same names.

Setup

First, you need to install rt itself. Using a personal library (e.g., echo 'R_LIBS_USER=~/.R/library' >> ~/.Renviron) is strongly advised.

devtools::install_github("rdatsci/rt")

Alternatively, if you start from scratch and do not have devtools installed, run the following command in your shell:

Rscript -e 'install.packages("devtools", repos = "http://cloud.r-project.org/")'
Rscript -e 'devtools::install_github("rdatsci/rt")'

The rt command line scripts are now installed in the subdirectory rt/bin of your R library (call .libPaths() in R if unsure about its location). You need to add this directory to your PATH variable, see the section below that applies to you.

On Linux

Add this directory to your PATH in your .bashrc, .zshrc or config.fish:

# bash
PATH=~/.R/library/rt/bin:$PATH

# zsh
path=(~/.R/library/rt/bin $path)

# fish
if test -d ~/.R/library/rt
    set -gx PATH $HOME/.R/library/rt/bin $PATH
end

On Windows

Add this directory to your PATH variable in the system environment via the control panel. As an alternative use the admin console command:

SETX /M PATH "%PATH%;path-to-rt-repository/win"

(Option /M changes the PATH in HKEY_LOCAL_MACHINE instead of HKEY_CURRENT_USER). If it does not work for you, try it without the /M option. In any case you need to open a new windows prompt or terminal windows in order to reload the PATH variable.

Continue for both Systems

After sourcing this file (or after a re-login) you should be all set to use rt.

To keep rt updated, you can let it maintain itself via rupdate by adding it to your collection file ~/.rt/packages. To do this, first initialize an empty collection with

rt init

and then uncomment the respective line with your favorite text editor. To add more packages to your collection, see ?rupdate for a format description of this file. Note that packages with a git source will be kept in ~/.rt/git and only reinstalled if the remote repository has been updated.