Tony Tsai

May the force of science be with you

May 7, 2018 - 3 minute read - Comments - R

Setting PATH Variable for gs Command in RStudio

Update on 2018-07-05

From the discussion with Yihui Xie, if Ghostscript was installed via brew, Homebrew should automatically make symlinks to /usr/local/bin/gs which is already under the PATH. Hence there is no need to set PATH variable for gs. However, the following approach is useful for other commands that are not under the PATH.

These days I am using ImageMagick to convert multiple pdfs (or pngs) into an animation gif to demonstrate the algorithm that I proposed for estimating epidemic onset. The convert command needs to call the gs command from Ghostscript. I successfully set PATH variable for gs command in my .zshrc file and the result of echo $PATH in the Terminal shows that the path to the bin directory of Ghostscript is in the PATH variable.

$ echo $PATH

Now we can easily find the gs command in the Terminal by typing

$ which gs

And the convert command also works fine in the Terminal.

However, the system() call to the convert command can not work in RStudio. The problem lied in the fact that by default OSX GUI applications don’t inherit the environment variables set in the bash .profile file.

Hence, as shown in following command, the PATH variable in RStudio doesn’t contain the path to the bin directory of Ghostscript. (It is noted that the output of base::system() cannot be captured in Rmarkdown. See the issue of knitr package and the SO question asked by Yihui Xie. So we will use the following system() function to substitute the base::system() function, and then knitr will be able to capture the output of system().)

  system <- function(...) cat(base::system(..., intern = TRUE), sep = "\n")
system("echo $PATH")
## /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:/opt/X11/bin

And the system() call cannot find the gs command in RStudio.

system("which gs")
## /usr/local/Cellar/ghostscript/9.23/bin/gs

The same problem was reported in RStudio Support in December 2013. From the discussion, we know one solution is to open RStudio in the Terminal to inherit the environment variables set in the bash .profile file; however, this way to start RStudio is very inconvenient. Alternatively we can set PATH variable to gs in the user .Renviron file which is in the user’s home directory ~. The file R_HOME/etc/Renviron contains environment variables set by R in the configure process. Values in this file can be overridden in user environment file, hence do not change R_HOME/etc/Renviron itself. Type ?Startup in R console to see details on the startup mechanism of an R session.

usethis has a useful helper function to modify .Renviron. Typing usethis::edit_r_environ() open the user .Renviron file for editing. Then add following PATH variable to the .Renviron file.


Save the .Renviron file and reopen RStudio to take effect.

Alternatively we can add the path to the gs command as the PATH variable in the Renviron file for RStudio. Firstly find the Renviron file: R_HOME/etc/Renviron under the directory of R_HOME.
## [1] "/usr/local/Cellar/r/3.5.1/lib/R"
Then edit the Renviron file and add following PATH environment variable.
Save the Renviron file and reopen RStudio.

Now check the PATH variable setting again in RStudio.

[1] "/usr/local/Cellar/ghostscript/9.23/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:/opt/X11/bin"

As you can see, the path to the bin directory of Ghostscript is now in the PATH variable. And we can find the gs command in RStudio and of course, the convert command also works fine in RStudio.

system("which gs")
## /usr/local/Cellar/ghostscript/9.23/bin/gs