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Question Detail

Whenever I change the library path order using the .libPaths() function, it reverts back to the default if I restart R. How can I change this permanently? I am working on a Linux computing cluster (I don’t have admin rights) so, I want to add my local library to R permanently.

I have to do this every time I start R

.libPaths(c("/home/...","/home...","/local/library"))

Question Answer

For completeness, and as I can’t show this in a comment:

  1. Default on all Debian and Ubuntu systems with the shipped R package:

    [email protected]:~$ R -q -e ‘print(.libPaths())’
    R> print(.libPaths())
    [1] “/usr/local/lib/R/site-library” “/usr/lib/R/site-library”
    [3] “/usr/lib/R/library”
    R>
    R>

  2. Which we can alter by modifying R_LIBS_SITE:

    [email protected]:~$ R_LIBS_SITE=”/usr/lib/R/Library” R -q -e ‘print(.libPaths())’
    R> print(.libPaths())
    [1] “/usr/lib/R/library”
    R>
    R>

  3. But modifying R_LIBS does not work:

    [email protected]:~$ R_LIBS=”/usr/lib/R/Library” R -q -e ‘print(.libPaths())’
    R> print(.libPaths())
    [1] “/usr/local/lib/R/site-library” “/usr/lib/R/site-library”
    [3] “/usr/lib/R/library”
    R>
    R>
    [email protected]:~$

See help(Startup) for the full and detailed treatment. On Debian and Ubuntu we have been setting these three directories as the default for well over a decade. As it is set via R_LIBS_SITE here, this is the variable you need to alter here. In general, you need to override the variable holding the value and you may not know ex ante which one that is.

As for the original answer, on Debian and Ubuntu we use the file /etc/R/Renviron. As help(Startup) details, you can set any number of ways to alter this permanently for your startup — and all these points hold for all different OSs:

  1. Alter the system files such as Renviron or Renviron.site if you have the proper permissions
  2. Else alter the per-user file ~/.Renviron
  3. Alternatively, alter the environment variables R_LIBS or R_LIBS_USER or R_LIBS_SITE at the system level if you have the proper permissions
  4. Else alter the variables R_LIBS or R_LIBS_USER or R_LIBS_SITE at the user level.
  5. Lastly, call .libPaths(...new path to be added here...) in your R startup files as e.g. in .Rprofile.

Do see help(Startup) for a fuller-length discussion.

find the Rprofile file (no dot) in R installation folder

find -name Rprofile

#Getting something like:
#lib/R/library/base/R/Rprofile

Open the file and search for:

invisible(.libPaths(c(unlist(strsplit(Sys.getenv("R_LIBS"), ":")),
                      unlist(strsplit(Sys.getenv("R_LIBS_USER"), ":") )
                      )))

comment other paths and add your desired path

invisible(.libPaths(c(#unlist(strsplit(Sys.getenv("R_LIBS"), ":")),
                      #unlist(strsplit(Sys.getenv("R_LIBS_USER"), ":") )
                      "/home/users/username/R/4.0.1/lib/R/library" # desired path
                      )))

This can be useful also: (for .bashrc file)

export R_LIBS='/home/users/username/R/4.0.1/lib/R/library'
export R_LIBS_USER='/home/users/username/R/4.0.1/lib/R/library'

2 major solutions:

  1. In .Rprofile you could leave code that sets .libPaths()

  2. Just set the appropriate environment variable such as R_LIBS in Windows or R_LIBS_SITE= in Linux, etc, to whatever you like, e.g.

     R_LIBS=C:/R/Library 
    

On Mac, I find that in a ‘fresh’ installation there is no user library and packages are all installed in the version-specific system library. Eventually, a user library is created (possibly accidentally or via an RStudio prompt) and is set to the default location for future package installations. So, if you’re not paying close attention you end up with some packages installed in the system library and some in the user library.

The user library is listed first and the system library is listed second:

.libPaths()
> [1] "/Users/<username>/Library/R/3.6/library"                         
> [2] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library"

I like to keep everything in one place (the system library), so to accomplish this (permanently) I do the following:

In a Terminal window, create a .Rprofile file in your user directory:

nano ~/.Rprofile

In that file, add the following line of R code:

.libPaths( c(.libPaths()[2], .libPaths()[1]) )

Alternatively, add a similar line of R code but with hardcoded paths:

.libPaths( c("/Library/Frameworks/R.framework/Versions/3.6/Resources/library", "/Users/<username>/Library/R/3.6/library") )

Replace <username> with your actual username. Then Ctrl-O (save) and Ctrl-X (exit) that file.

Either line switches the order of the paths listed above, so that path [2] (system) is first (Default) and path [1] (user) is second.

Importantly, by putting this line of code in your user’s .Rprofile it will be run every time R starts and you (hopefully) won’t have to worry about this again.

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