My R setup on Debian

June 18, 2018

  R Linux Debian Setup

  base

Kevin Cazelles  

David Beauchesne  

6min


R 3.5.0 “Joy in playing” was released April 23rd this year. It took a couple of weeks before it was made available on Debian testing due to the work required to rebuild the packages and as a Debian user that spend a lot of time on R, I am extremely grateful to the work of Dirk, Michael and Johannes on this!

I thought it was a good opportunity to write few notes about my R setup. Nothing really special or tricky and I guess more advanced users proceed otherwise, yet it is nonetheless simple and functional 😄! In this post I’ll go over two different aspects:

  1. the way I install R and the packages I use,

  2. how I customized my R’s startup.

How do I install and the package I use?

As mentioned in a previous post, I am currently working on Debian testing and use apt-get to install my software which includes R:

# this lines and the following may need to be run in super user mode
$ apt-get install r-base r-recommended r-base-dev

I use the default location to store the core packages, i.e. /usr/lib/R/library/. After the installation of the core packages, I configure Java for R (see Java support on the manual for more details):

$ R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/

Then I install all CRAN packages available via apt-get:

$ apt-get install "^r-cran-.*"

This actually is very helpful to ensure that dependencies are properly installed! The path to those packages is /usr/lib/R/site-library/ (again default behavior) It is true though that I do not use all these packages, but:

  1. I use a fair portion of them (directly or as dependencies of other packages I use)

  2. It is really quick to install (quicker than installing them from inside R)

  3. I have space on my computer and it only takes one single line on my script whereas a selection would probably have taken tens 😄!

For the remaining packages (not packaged specifically for Debian), I use the classical ìnstall.packages() for packages on CRAN and devtools::install_github() for GitHub packages. I do not use package from other repositories. For those packages, I have created a small gist to gather them and I edit it each time I’ve found a package relevant for my research. In order to install this package I get the gist (an R script) and execute it:

$ git clone https://gist.github.com/aaa83151e9d12cc07fbe379e2c32a385.git /tmp/pkgsR
$ sudo Rscript /tmp/pkgsR/myPackages.R

The path to these packages is /home/kevcaz/R/x86_64-pc-linux-gnu-library/3.5 this is not the default behavior but a path commonly used. So, yes, in total I use 3 different paths to my R packages 😃:

R>> .libPaths()
[1] "/home/kevcaz/R/x86_64-pc-linux-gnu-library/3.5" "/usr/lib/R/site-library"                        "/usr/lib/R/library"

This is actually quite handful, especially to remember how a given package was installed:

R>> find.package("stats")
[1] "/usr/lib/R/library/stats"

R>> find.package("Rcpp")
[1] "/usr/lib/R/site-library/Rcpp"

R>> find.package("drat")
[1] "/home/kevcaz/R/x86_64-pc-linux-gnu-library/3.5/drat"

Well, I very much like it that way 😸! Two notes to conclude this section. First, in the near future I may consider the neat drat package to add packages available on GitHub. Second, if you are interested in reproducing this installation, have a look at my installDebian.sh gist.

Now that R is installed let’s see how to customize the launch process.

My R’s Startup

When you type R and enter in your favorite terminal or when you open RStudio, many things happen before you can enter your first line of code for the session (even more for RStudio I guess). This is the startup process. It is thoroughly explained here (also available in R using help(Startup)) and in this post on R Views. Below I’d like to explain how I take advantage of the possibility of personalizing it to make my use of R more comfortable. Basically, during the launch process I:

  1. set up a couple of options (including default packages loaded),
  2. tweak some paths,
  3. get nice hello and good bye messages (the most important part!).

For what I do, you simply must retain how to locate Renviron. First, call R.home:

R>> R.home()
[1] "/usr/lib/R"

Renviron is in /etc, so for me /usr/lib/R/etc:

$ ls /usr/lib/R/etc
javaconf  ldpaths  Makeconf  Renviron  Renviron.orig  Renviron.site  Renviron.ucf  repositories  Rprofile.site

Once you have opened it (it may require the super user mode though), you’ll find many options you can change. I suggest you do not change anything and rather add a new variable R_ENVIRON to point to a site file where you will do the changes without touching the original file (well this is actually the purpose of this variable). In my case I added:

R_ENVIRON = "/usr/lib/R/etc/Renviron.site"

It is not mandatory but it is pretty common to locate where you add your chnages next to the default one. On Debian we actually get an empty Renviron.site file:

##                                              Emacs please make this -*- R -*-
## empty Renviron.site for R on Debian
##
## Copyright (C) 2008 - 2017  Dirk Eddelbuettel and GPL'ed
##
## see help(Startup) for documentation on ~/.Renviron and Renviron.site

# ## Example ~/.Renviron on Unix
# R_LIBS=~/R/library
# PAGER=/usr/local/bin/less

# ## Example .Renviron on Windows
# R_LIBS=C:/R/library
# MY_TCLTK="c:/Program Files/Tcl/bin"

# ## Example of setting R_DEFAULT_PACKAGES (from R CMD check)
# R_DEFAULT_PACKAGES='utils,grDevices,graphics,stats'
# # this loads the packages in the order given, so they appear on
# # the search path in reverse order.

## # We comment out this line in the default Renviron, you can re-enable it here
## # @R_PLATFORM@ can be eg x86_64-pc-linux-gnu, see /etc/R/Renviron for R_PLATFORM
## # @MAJ_MIN_VERSION@ is likely something like '3.4', see /etc/R/Renviron too
#R_LIBS_USER=${R_LIBS_USER-'~/R/@R_PLATFORM@-library/@MAJ_MIN_VERSION@'}

Thanks Dirk for this! As you can read, several changes are possible and all the parameter found in Renviron may be used. In my case I added two lines

R_PROFILE_USER = "~/.Rprofile"
R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/3.5'}

The latter indicates the path to packages installed with ìnstall.packages(), while the former points to another file where I do most of the tweaks! Here it is (also available on ):

#### KevCaz's .Rprofile
## To refresh => remove the .RData file otherwise .First is found in there
## or use R --no-restore

##-- Set the RNG
set.seed(1987)

##-- options (exlicit enough)
options(
  prompt = "R>> ",
  continue = "+... ",
  width = 160,
  max.print = 2000,
  repos = "https://cran.wu.ac.at/",
  stringsAsFactors = FALSE
)
# Default packages list including my own packages with functions I often use!
options(defaultPackages=c(
    getOption("defaultPackages"),
    "inSilecoMisc",
    "devtools",
    "knitr",
    "magrittr",
    "graphicsutils",
    "rmarkdown"
    ))
##-- X11 options
grDevices::X11.options(width=10, height=10)


##-- few useful functions
reset <- function() system('reset')
nautilus <- function(x='.') system(paste0('nautilus ', x))
deco <- function(char = "-", n = 10) paste(rep(char, n), collapse="")

##-- function triggered when starting a new session / a Hello function
.First <- function(){
    cat("\n", paste0(deco("=", n = 28), ">>"), " KevCaz 92 Hijo ",
    paste0("<<", deco("=", n = 28)), "\n >>", date(), " \n\n") ;
}

##-- function triggered when exiting a new session / a Good Bye function
.Last <- function(){
    graphics.off()
    cat("\n", paste0(deco("~", n = 28), "<") , " Até mais KevCaz! ",
    paste0(">", deco("~", n = 28)),"\n") ;
}


That’s it! Hope this helps! See you next post!   🚀



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