Customizing your R command line experience

I’ve come to appreciate how powerful R is for working with data, but I find it has some pretty awkward and clunky defaults that make every interaction with the command line kind of aggravating.

mike@sleepycat:~$ R

R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages("tidyverse")
Warning in install.packages("tidyverse") :
  'lib = "/usr/lib/R/library"' is not writable
Would you like to use a personal library instead?  (y/n)
Save workspace image? [y/n/c]: n

Here you can see a few things that I’m not a fan of. First up, uppercase commands are just weird. Second, holy moly that’s a lot of blah blah to give me a repl.

Next, this warning about the non-writable directory; /usr will always be read only and owned by root. Why even try to write there?

Accepting the offer to use a “personal library” translates to creating a directory like ~/R/x86_64-pc-linux-gnu-library/3.4, which is another annoyance. Why isn’t this a hidden directory? Why must I be forced to look at this R directory every time I see my home folder?

Finally, if I’m doing something more than a quick experiment, I’ll write a script in a text file so I can track changes to it with git rather than saving my work in some opaque .RData file. Given that, having R always asking to save my workspace is deeply irritating.

We can pick off a few of these problems with a simple alias, by adding the following to your ~/.bashrc file:

alias r="R --no-save --quiet"

This immediately gives us a far more civilized experience getting in and out of R: I can launch R with a lowercase r command and then exit without a fuss with Ctrl+d (signaling the end of input). The --quiet kills the introductory text while --no-save gets rid of the “Save workspace image?” nag.

mike@sleepycat:~$ r

This is a good start but goofy stuff like where to save your libraries will need to be solved another way: your Rprofile. While starting up R looks for certain configuration files one of them being ~/.Rprofile.

I’ve created a hidden folder called .rlibs folder in my home directory which my Rprofile then sets as my chosen place to save libraries among a few other things likes setting a default mirror and loading and saving my command history.

Here is what’s working for me:

# Load utils so we can use it here.

# Save R libraries into my /home/$USER/.rlibs instead of somewhere that
# requires root privileges:

# Stop asking me about mirrors, and always use the https
# cran mirror at
local({r <- getOption("repos")
      r["CRAN"] <- ""

# Some reasonable defaults:

# Run at startup
.First <- function(){
  # Load my history if this is an interactive session
  if (interactive()) utils::loadhistory(file = "~/.Rhistory")
  # Load the packages in the tidyverse without warnings.
  # suppressMessages(library(tidyverse))

# Run at the end of your session
.Last <- function(){
  if (interactive()) utils:::savehistory(file = "~/.Rhistory")

This little foray into R configuration has made R really nice to use from the command line. Hopefully this will be a decent starting point for others as well.


Installing R-Studio on Ubuntu 16.10

rstudioInstalling things on Linux is either really easy, or a yak shave with surprisingly little between those extremes.

It seems that Ubuntu 16.10 has removed Gstreamer 0.10 from the repos and replaced it with Gstreamer 1.0, which is great… until you need to install R-Studio.

While the R-Studio people are aiming to drop the Gstreamer dependency, for the moment, as of 16.10, installing it has fallen into the yak-shave category.

Installing R-Studio works fine, but if you try to run (from the terminal) it you will get the error:

rstudio: error while loading shared libraries: cannot open shared object file: No such file or directory

We can see that it’s failing to load Gstreamer, but since it’s been removed from the Ubuntu repos fixing this will mean getting those packages elsewhere.

To start with, we can download the latest R-studio daily build and install it using dpkg:

$ wget
$ sudo dpkg -i rstudio-1.0.124-amd64.deb

The dpkg command can also query the package to display information about it. If we use the uppercase I option we can confirm that this package requires exactly version 0.10 of libgstreamer:

dpkg -I rstudio-1.0.124-amd64.deb 
 new debian package, version 2.0.
 size 98840122 bytes: control archive=42847 bytes.
     554 bytes,    12 lines      control              
  163246 bytes,  1548 lines      md5sums              
     198 bytes,    10 lines   *  postinst             #!/bin/sh
     158 bytes,    10 lines   *  postrm               #!/bin/sh
 Package: rstudio
 Version: 1.0.124
 Section: devel
 Priority: optional
 Architecture: amd64
 Depends: libjpeg62, libedit2, libgstreamer0.10-0, libgstreamer-plugins-base0.10-0, libssl1.0.0,  libc6 (>= 2.7)
 Recommends: r-base (>= 2.11.1)
 Installed-Size: 526019
 Maintainer: RStudio <>
 Description: RStudio
  RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, and workspace management.

Debian (which Ubuntu is based on) has the old Gstreamer packages we need to satisfy those dependencies, so we can get them from there. If you need something other than the AMD64 see here and here. The if you have a 64bit machine, you can download and install like this:

# download with wget
$ wget
$ wget

# Now install with dpkg
$ sudo dpkg -i libgstreamer0.10-0_0.10.36-1.5_amd64.deb
$ sudo dpkg -i libgstreamer-plugins-base0.10-0_0.10.36-2_amd64.deb

While that solves R’s problems, we now have one of our own. We’ve purposefully installed old packages and don’t want Ubuntu’s package manager to enthusiastically upgrade them next time we update.
To resolve that problem will put a hold on them with apt-mark:

$ sudo apt-mark hold libgstreamer-plugins-base0.10-0
libgstreamer-plugins-base0.10-0 set on hold.
$ sudo apt-mark hold libgstreamer0.10
libgstreamer0.10-0 set on hold.

And we can check the packages that are on hold with:

$ sudo apt-mark showhold

Hopefully that saves someone some Googling.
Now that’s working, it’s time to play with some R!