Rpkg: command-line interface to the R package manager

• What is this?
  • Show-off example
• Installation
• Usage
  • Examples

What is this?

Rpkg is a simple command-line interface to the R package manager.

Typically, R user install packages in the console, using functions like install.packages(). I wrote this tool because I find it inconvenient to open an R console to manage the R package library. It is especially useful for scripting, which in turn can make it easier to encapsulate and reproduce your development or research environment.

The vision for Rpkg is twofold:

1. Create a simple, unified interface to the package management features that are built into R.
2. Reach a stable, complete 1.0 interface that will not need to change much. In 10 years, when GitHub has gone the way of SourceForge, you should be able to download and run this program without serious problems, as long as R itself does not undergo radical changes (which it historically has not).

If you have any suggestions, requests, or bugs to report, please feel free to file an issue for them. You are also welcome to submit a pull request directly. If you would like to contribute but don't know where to start, see the file TODO.md some of the feature roadmap, or the various "TODO" comments in the code.

Show-off example

$ Rpkg install forecast

Installing package into ‘/usr/local/lib/R/3.4/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/forecast_8.1.tar.gz'
Content type 'application/x-gzip' length 783567 bytes (765 KB)
==================================================
downloaded 765 KB

* installing *source* package ‘forecast’ ...
** package ‘forecast’ successfully unpacked and MD5 sums checked
** libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (forecast)

The downloaded source packages are in
	‘/private/var/folders/4j/n8nxnsy12y92t475g318yptm0000gn/T/RtmpKRM4Ne/downloaded_packages’

Installation

1. git clone this repo or download and extract a tagged release.
2. make or make setup
3. make install, using sudo if necessary for your system. By default this installs to /usr/local/bin/Rpkg, but you can change that location with the RPKG_INSTALL_PREFIX environment variable.

Uninstall with make uninstall.

Note that installation requires a symlink tothis repo, because the Library path is found dynamically. Future releases will use Cmake (or a similar tool) to configure and encode the correct paths so thatRpkg can be copied, not linked.

I've personally tested the Makefile on the MacOS version of GNU Make (version 3.81) and vanilla GNU Make 4.2.1. Your mileage might vary with BSD Make or other/ancient Makes.

I've also only personally tested this on R version 3.4. I don't think I'm using anything specific to recent R versions, but if anything breaks in old versions, please file an issue.

This script is intended to be run by Rscript --no-save. Note that Rscript already implies --slave and --no-restore. It does source your init file, i.e. Rprofile. This is to ensure that any user configuration like options(repos = c(CRAN = "https://cloud.r-project.org")) is respected. HOWEVER, Rpkg is not robust to excessive tinkering, and if something breaks try running Rscript --no-save --no-init cli/Rpkg before reporting a bug.

The default CRAN repository when using this tool is "https://cloud.r-project.org". The option to use a non-CRAN repository will become available after proper command-line parsing has been implemented.

Usage

Using Rpkg is much like any other package manager: yum, brew, pip, npm, etc. Commands take the form:

Rpkg <main_options> <subcommand> <subcommand_options> <arguments>

The main_options are Unix-style flags (even on Windows, they are currently hardcoded to use dashes and not slashes) that change the behavior of the main Rpkg command. The subcommand_options apply specifically to the subcommand being called.

The Rpkg help subcommand prints a list of available commands and options for the Rpkg script itself. In the future, Rpkg help <subcommand> will print similar information for the listed subcommand.

As a reference, the Rpkg help string from the source code is copied below:

Rpkg version %s

Commands:
    help [ SUBCOMMAND ]
        Get help for SUBCOMMAND.

    ( install | add ) PKG_NAME [ PKG_NAME ... ]
        Install packages. See R help for install.packages().

    ( uninstall | remove ) PKG_NAME [ PKG_NAME ... ]
        Uninstall packages. See R help for remove.packages().

    ( update | upgrade ) ( --all | [ PKG_NAME [ PKG_NAME ... ] ] )
        Update packages. See R help for update.packages(). PKG_NAME is required 
        if --all is not specified.

    reinstall PKG_NAME [ PKG_NAME ... ]
      Remove then reinstall packages.

    outdated
      Print a list of outdated packages.

    list
      Print a list of installed packages.

    info PKG_NAME [ PKG_NAME ... ]
      Print package info from the repository.

    search ( STRING | /REGEX/ )
      Search for a package name in the repository. Regex is PCRE, and is 
      case-sensitive only if it contains an upper-case character.

Options:
    Long options that accept arguments can be specified with
        --option=ARG
    or
        --option ARG
    interchangeably.

    -V
    --version      Print version info and exit.

    -h
    --help         Print this help and exit.

    -v
    --verbose       options(\"verbose\") <- TRUE

    --type=TYPE     options(\"pkgType\") <- $TYPE

    -j NJOBS
    --jobs=[NJOBS]
    --ncpu=[NJOBS]  options(\"Ncpu\") <- $NJOBS

Examples

Install caret and shiny from CRAN:

Rpkg add caret shiny

Update caret and shiny to latest version on CRAN:

Rpkg update caret shiny

Update all packages:

Rpkg update --all

Uninstall caret and shiny:

Rpkg remove caret shiny

Check for outdated packages, get info about the forestFloor package, list installed packages:

Rpkg outdated
Rpkg info forestFloor
Rpkg list

Search CRAN:

Rpkg search ggplot
Rpkg search '/^z[^aeiou]/' # pattern is a regular expression if wrapped in slashes
Rpkg search '/^GG/'        # case-sensitive only if the pattern has an upper case character