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

Question

I am running R on Windows, not as an administrator. When I install a package, the following command doesn't work:

> install.packages("zoo")
Installing package(s) into ‘C:/Program Files/R/R-2.15.2/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  'lib = "C:/Program Files/R/R-2.15.2/library"' is not writable

To install a package, I have to specify a library location:

install.packages("zoo", lib="C:/software/Rpackages")

To load a package, I also have to specify the library location:

library("zoo", lib.loc="C:/software/Rpackages")

All of this is OK, but I wanted to see if I could add C:/software/Rpackages to the library path somehow and thus not have to type it each time.

As I searched online, I found that one way to do this is to edit the Rprofile.site file and to add the line

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

However, after doing this, and starting RStudio, this is the output that I get

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

The .libPaths command that I added to the Rprofile.site doesn't seem to have had any effect! Why is this the case? Or more importantly, how can I fix the problem so that I can install and load packages without typing in the library location?

Note: if I start RStudio the .libPaths() command seems to work as it is supposed to

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

Isn't that strange?

Competent

Can you expand a bit on how exactly install.packages("zoo") doesn't work? Error message, etc.? – Ilene

@Ilene I added the error message when I try install.packages("zoo")---but that is not my real question, which is about why .libPaths() in Rprofile.site doesn't work. – Competent

Do you have the same trouble if you use RGui instead of R Studio? – Alfi

Why does R's library paths default to folders that need admin permissions?! Surely the user's home directory would be more sensible – Fideliafidelio

superuser.com/questions/749283/… Edit ~/.Renviron R_LIBS_USER=/some/path – Cholecalciferol

Answer 1

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/
 

Cutaway

I needed to reverse the c() vector to ensure new libraries go to the custom folder – Fideliafidelio

Excellent point. In fact the .libPaths-function have the same effect by default. There is also a difference between OSes in how trailing slashes are handled. (Not OK on Windows). Other options exist. See ?.libPaths – Cutaway

The new path has to exist in the file system actually, otherwise it won't be added to the library path – Husband

Another good point. Although the function name suggests otherwise, you can first check with file.exists and proceed only if the path is not missing. – Cutaway

I did this and it works, but it seems that I have to change the path every time I start R. Is that the same for others? – Taxdeductible

Have you looked at ?Startup to see your (many) options for making this change permanent? You may need to refer also to the RStudio manuals if they are not respecting or perhaps overwriting the .libPaths() settings. – Cutaway

?Startup indicates the ‘R_HOME/etc/Renviron.site’ and ‘R_HOME/etc/Rprofile.site’. On linux I do not have this. I have etc coming before R_home as in /etc/R/Renviron.site and /etc/R/Rprofile.site. Edit these files does not do anything when I run R with sudo R. I don't need to run with sudo all the time but building bindings to another package I do when making. – Ordinarily

Nevermind there are symlinks in /usr/lib/R/etc so maybe that is why? This may be why its good to indicate where these files are when writing SO responses. – Ordinarily

Answer 2

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.

Maidy

Definitely the proper solution. The only catch is if your user is not a admin (likely the case if you're having this problem to begin with), you have to change your environment variables via Control Panel->User Accounts->User Accounts->Change my environment variables. – Noisette

Do you (happen to) know the equivalent in Linux command line? – Quietus

Sure, just set these as your shell variables (in bash you can edit .bash_profile and/or .bashrc). See here: unix.stackexchange.com/questions/117467/… For setting these for current session only type in console export R_LIBS_USER='directory_of_your_choice' – Diapositive

Magic solution! this worked perfect to me in RStudio with Windows7 – Border

Confirm, this is the correct solution under Windows 8.1 R-version 3.2.2 – Regen

I did exactly this after reading this thread but to no avail. I wanted to add the "D:\RPacks" path which shows up as first path after typing '.libPaths()' but the packages are still installed in this standard folder. I have Windows 7, latest version of R and work within the RStudio environment. – Adena

I was struggling with this until I realized the environmental variable cannot be quoted. – Amphibole

instead of setting the variable through control panel, I have modified the default value of R_LIB_USER in the Rprofile file. Here the solution: I came up with a similar approach, the solution is presented in as a solution to this question #31708441 – Anglicist

This is for me the simplest solution and works best. If user does not have access to environment variables though (like if user doesn't have admin privilege), I guess @Anglicist 's suggestion to set environment variables R_LIBS_USER in Rprofile.site file would work too. – Ricotta

my R_LIBS_USER value and the return value of .libPaths() is different – Swoon

Note that you may need to log out and back in again before the change shows up. – Roberto

In my case .libpath("path") did not work, but this answer 1. Set .Rprofile worked. Does anybody understand? – Goffer

It might help to use %-"conversion specifiers" (see stat.ethz.ch/R-manual/R-devel/library/base/html/libPaths.html). So to get ~/.local/lib/R/x86_64-pc-linux-gnu-library/3.6 one would write ~/.local/lib/R/%p-library/%v. – Lissie

For a Windows step-by-step version, see #31708441 – Butylene

Answer 3

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"

Competent

This doesn't work for me (neither does the solution from BondedDust). I created a txt file and saved it as .Rprofile in the folder from getwd(). – Alderney

@Alderney I believe that we are saying the same thing. – Competent

R reads .Rprofile from your HOME directory not from your CURRENT directory. – Stomacher

I came up with a similar approach, the solution is presented in as a solution to this question #31708441 – Anglicist

To find the home directroy issue the r command Sys.getenv("HOME") in the r console. I am not sure if you get the desired output. I think the desired output is that what 42 showed in his answer https://mcmap.net/q/107531/-change-r-default-library-path-using-libpaths-in-rprofile-site-fails-to-work . He uses .libPaths in a slighly different way. – Brythonic

@Stomacher - R reads .Rprofile from the current directory if it is present instead of the one in the home directory, and if that doesn't exist, it falls back to the Rprofile.site – Selfreliance

Answer 4

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

Edit ~/.Renviron

R_LIBS_USER=/some/path

Cholecalciferol

Answer 5

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" > .Renviron Make sure the spelling and 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.

Clarify

Answer 6

If you do not have admin-rights, it can also be helpful to open the Rprofile.site-file located in \R-3.1.0\etc and add:

.First <- function(){
  .libPaths("your path here")
}

This evaluates the .libPath() command directly at start

Stile

Answer 7

On Ubuntu, the recommended way of changing the default library path for a user, is to set the R_LIBS_USER variable in the ~/.Renviron file.

touch ~/.Renviron
echo "R_LIBS_USER=/custom/path/in/absolute/form" >> ~/.Renviron

Pinon

Answer 8

just change the default folder for your R libraries in a directory with no Administrator rights, e.g.

.libPaths("C:/R/libs")

Soredium

Answer 9

I've had real trouble understanding this. gorkypl gave the correct solution above when I last re-installed my OS & Rstudio but this time round, setting my environment variable didn't resolve.

Uninstallled both R and Rstudio, creating directories C:\R and C:\Rstudio then reinstalled both.

Define R_LIBS_USER user variable to your prefered directory (as per gorkypl's answer) and restart your machine for User variable to be loaded. Open Rstudio, errors should be gone.

You can also use Sys.setenv() to modify R_LIBS_USER to the path of your alternative library which is easier and does not need to restart your computer.

To see what R_LIBS_USER is set to: ?Sys.getenv()

Reading help(Startup) is useful.

Illustrious

Answer 10

If your default package library has been changed after installing a new version of R or by any other means, you can append both the libraries to use all the packages with the help of the commands below. Get the existing library path :

.libPaths()

Now,set the existing and the old path :

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

Hope it helps.

Lilianaliliane

Answer 11

I had the same problem and I run into this. If you want to create another location c("C:/Users/mynewlocation") should be working as well. As mentioned in here "You should be able to right-click on the Rstudio.exe icon, click Properties, and select an option to always run Rstudio as administrator. Be sure you use that same icon whenever you want to open Rstudio."

    myPaths <- .libPaths()   # get the paths
myPaths <- c(myPaths[2], myPaths[1])  # switch them
.libPaths(myPaths)  # reassign them

Discolor

Answer 12

I read the readme. In that they mentioned use .libPaths() in command line to check which paths are there. I had 2 library paths earlier. When I used the command .libpath("C:/Program Files/R/R-3.2.4revised/library") where I wanted, it changed the library path. When I typed in .libPaths() at the command line again it showed me the correct path. Hope this helps

Czarra

Answer 13

getwd()
# [1] "C:/Users/..../software/My R studio"

copy the above link with double inverted comma

.libPaths(new="C:/Users/..../software/My R studio")

Your default path will change for installing pakages

Aloeswood

Answer 14

If you want to change your library path permanently (without calling .libPath() every time when entering in R, this works for me:

1. create .Rprofile under your home directory. (~/.Rprofile)

2. type .libPaths(c( .libPaths(), "your new path" )) in .Rprofile file, save.

3. open R (any directory) and check, just type .libPaths(), you can find your libaray path is updated!

Fakery

Answer 15

Since most of the answers here are related to Windows & Mac OS, (and considering that I also struggled with this) I decided to post the process that helped me solve this problem on my Arch Linux setup.

Step 1:

• Do a global search of your system (e.g. ANGRYSearch) for the term Renviron (which is the configuration file where the settings for the user libraries are set).
• It should return only two results at the following directory paths:
  
  1. /etc/R/
     
  2. /usr/lib/R/etc/
     NOTE: The Renviron config files stored at 1 & 2 (above) are hot-linked to each other (which means changes made to one file will automatically be applied [ in the same form / structure ] to the other file when the file being edited is saved - [ you also need sudo rights for saving the file post-edit ] ).

Step 2:

• Navigate into the 1st directory path ( /etc/R/ ) and open the Renviron file with your favourite text editor.
• Once inside the Renviron file search for the R_LIBS_USER tag and update the text in the curly braces section to your desired directory path.
  
  EXAMPLE:
  ... Change From ( original entry ):
  R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/4.0'}
  ... Change To ( your desired entry ):
  R_LIBS_USER=${R_LIBS_USER-'~/Apps/R/rUserLibs'}
  

Step 3:

• Save the Renviron file you've just edited ... DONE !!

Navicular

Answer 16

I was looking into this because R was having issues installing into the default location and was instead just putting the packages into the temp folder. It turned out to be the latest update for Mcaffee Endpoint Security which apparently has issues with R. You can disable the threat protection while you install the packages and it will work properly.

Appleby