Change R default library path using .libPaths in Rprofile.site fails to work

Question

The proper solution is to set environment variable R_LIBS_USER to the value of the file path to your desired library folder as opposed to getting RStudio to recognize a Rprofile.site file.

To set environment variable R_LIBS_USER in Windows, go to the Control Panel (System Properties -> Advanced system properties -> Environment Variables -> User Variables) to a desired value (the path to your library folder), e.g.

Variable name: R_LIBS_USER 
Variable value: C:/software/Rpackages  

If for some reason you do not have access to the control panel, you can try running rundll32 sysdm.cpl,EditEnvironmentVariables from the command line on Windows and add the environment variable from there.

Setting R_LIBS_USER will ensure that the library shows up first in .libPaths() regardless of starting RStudio directly or by right-clicking an file and "Open With" to start RStudio.

The Rprofile solution can work if RStudio is always started by clicking the RStudio shortcut. In this case, setting the default working directory to the directory that houses your Rprofile will be sufficient. The Rprofile solution does not work when clicking on a file to start RStudio because that changes the working directory away from the default working directory.

I generally try to keep all of my packages in one library, but if you want to add a library why not append the new library (which must already exist in your filesystem) to the existing library path?

.libPaths( c( .libPaths(), "~/userLibrary") )
 # obviously this would need to be a valid file directory in your OS
 # min just happened to be on a Mac that day

Or (and this will make the userLibrary the first place to put new packages):

.libPaths( c( "~/userLibrary" , .libPaths() ) )

Then I get (at least back when I wrote this originally):

> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/2.15/Resources/library"
[2] "/Users/user_name/userLibrary"  

The .libPaths function is a bit different than most other nongraphics functions. It works via side-effect. The functions Sys.getenv and Sys.setenv that report and alter the R environment variables have been split apart but .libPaths can either report or alter its target.

The information about the R startup process can be read at ?Startup help page and there is RStudio material at: https://support.rstudio.com/hc/en-us/articles/200549016-Customizing-RStudio

In your case it appears that RStudio is not respecting the Rprofile.site settings or perhaps is overriding them by reading an .Rprofile setting from one of the RStudio defaults. It should also be mentioned that the result from this operation also appends the contents of calls to .Library and .Library.site, which is further reason why an RStudio- (or any other IDE or network installed-) hosted R might exhibit different behavior.

Since Sys.getenv() returns the current system environment for the R process, you can see the library and other paths with:

Sys.getenv()[ grep("LIB|PATH", names(Sys.getenv())) ]

The two that matter for storing and accessing packages are (now different on a Linux box):

R_LIBS_SITE                          /usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library
R_LIBS_USER                          /home/david/R/x86_64-pc-linux-gnu-library/3.5.1/
 

I managed to solve the problem by placing the code in the .Rprofile file in the default working directory.

First, I found the location of the default working directory

> getwd()
[1] "C:/Users/me/Documents"

Then I used a text editor to write a simple .Rprofile file with the following line in it

.libPaths("C:/software/Rpackages")

Finally, when I start R and run .libPaths() I get the desired output:

> .libPaths()
[1] "C:/software/Rpackages"               "C:/Program Files/R/R-2.15.2/library"
[3] "C:/Program Files/RStudio/R/library"

https://superuser.com/questions/749283/change-rstudio-library-path-at-home-directory

Edit ~/.Renviron

R_LIBS_USER=/some/path

I found what I think is a solution here (thank you Carl Schwarz at SFU) for adding a personal library that is permanently (you don't have to define it each session) recognized whether using R or Rstudio, and Rstudio treats it as the default on my Mac machine. I hadn't seen it laid out this explicitly on SO, so I summarized the steps they provided, for Windows and then for Mac.

For a Windows 7 OS:

1. Create a directory on the drive where you want to have your personal library, e.g. C:\User\Rlibs (or another that you have permissions to)

2. Search for/go to "Edit environment variable for your account" in the Windows search bar to edit control panel settings

3. Click "New..." in the middle of the "Environmental Variables" window

4. In the "New User Variable" window, type R_LIBS for the "Variable name", and the path to the personal library directory you created, e.g. C:\User\Rlibs

5. Click OK and you should see the Variable/Value pair in the User variables window

6. Click OK again

Now when you start R (or Rstudio) and type the command .libPaths() you should see the personal library you created as well as the R system library.

For Mac:

1. In your "Home" or "username" directory create a folder called Rlibs

2. Launch the Terminal application

3. Type: echo "R_LIBS=~/Rlibs"> .Renvrion Make sure case matches.

4. Type ls -a to see the full list of files in the directory, which should now include .Renvrion

5. Verify that the .Renviron file has been set properly: more .Renviron

Launch R/Rstudio and type .libPaths() and you should see the new path to your personal library.