Where should I set the variable PATH in R?

Question

I constantly need to call Tex Live binaries for compilation in R. However after the upgrade of Tex Live distribution, the path to current binaries needed to updated manually in the PATH(Sys.getenv("PATH")) variable.

As a single user on a Ubuntu system, which file should I update the value in, so that R gets the PATH correctly irrespective of whichever directory R is launched from.

One point I still don't gather is from where does R gets its site-wide (I mean for all users, even if faulty in saying so) PATH variable set, because no such variable name as "PATH" occur inside any files (Renviron, Renviron.site, Rprofile.site) in either of "R_HOME/etc/" and user's home directory? I also haven't set Sys.getenv("R_ENVIRON") and Sys.getenv("R_ENVIRON_USER") values.

I'd appreciate anybody's input here.

Answer 1

@JeffreyGoldberg's solution was close, but not quite right.

Rprofile files are interpreted as R code Renviron files can only contain name value pairs, and are not interpreted as R code

From the help for Startup:

Note that there are two sorts of files used in startup: environment files which contain lists of environment variables to be set, and profile files which contain R code.

I'm not sure if this question is asking specifically how one can set the site wide value of PATH, rather than PATH for one specific user, but there are three locations you can put these files.

1. A project directory (i.e., a directory you choose to launch R from)
2. HOME
3. R_HOME/etc

These locations are searched in the order numbered above. The first location can contain configurations specific to a project, the second contains those specific to a user, and the third, site wide configuration settings. When a file is found it is used, so local takes precedence over global. Don't think you can create a more specific version that simply updates what you've done in a more general configuration file. R_HOME/etc/Renviron is created on installation and should not be edited. You may create a file called R_HOME/etc/Renviron.site, but do not edit R_HOME/etc/Renviron.

To create a site wide value of PATH, you will want to set it in a file in R_HOME/etc. Here you can use either Renviron.site or Rprofile.site for the file name. For a file in R_HOME/etc, Do not use Renviron, Rprofile, .Renviron, or .Rprofile for the name of a profile or environment file in this location. You can find out what R_HOME is in an R session using R.home(), or Sys.getenv("R_HOME")

To create a PATH value for a single user, set it in a file in HOME, which you can find in your R session using Sys.getenv("HOME") or path.expand("~"). You can also just use "~" to refer to HOME. Here, an Renviron file should be ~/.Renvironand an Rprofile file ~/.Rprofile. Take note of the difference between how profile and environment files are named in your HOME directory vs. R_HOME/etc

To create a PATH for a single project, set it in a file in that project's top level directory. Name the files as you would in your home directory (.Rprofile or .Renviron).

If you are creating an Renviron file, the file should include the following line:

PATH=<your path>

< and > should not be included. An example would be:

PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin

If you are creating an Rprofile file, the file should include the following line:

Sys.setenv("<your path>")

again, don't include "<" or ">". An example would be:

Sys.setenv("/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin")

There are various ways of doing this that get and edit a PATH variable (e.g., tack on a new path at the end, or the beginning). You can also use the strategy of setting an environment variable if it doesn't already exist and/or doesn't contain something you want it to. I've come to prefer just setting up my path simply, and coding it directly.

One final note, if you run R from a command line interface, environment variables may be inherited from your shell. RStudio also has it's own startup sequence and may modify the end of your PATH variable. It should start as it is defined in your Rprofile or Renviron files. The R Console app itself has the fewest quirks with system environment variables, and should accept your path exactly as it is set with an Rprofile or Renviron file.