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    gt  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   gt   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    gt   libPaths    1   C  software Rpackages                 C  Program Files R R-2 15 2 library    Isn t that strange

User · Accepted Answer

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/

User · Answer

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  lt - function       libPaths  your path here       This evaluates the  libPath   command directly at start

User · Answer

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

User · Answer

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

User · Answer

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

User · Answer

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

User · Answer

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    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  Search for go to  Edit environment variable for your account  in the Windows search bar to edit control panel settings Click  New     in the middle of the  Environmental Variables  window 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 Click OK and you should see the Variable Value pair in the User variables window 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    In your  Home  or  username  directory create a folder called Rlibs Launch the Terminal application Type  echo  R LIBS   Rlibs  gt   Renvrion Make sure case matches  Type ls -a to see the full list of files in the directory  which should now include  Renvrion 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

User · Answer

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   gt  gt     Renviron

User · Answer

If you want to change your library path permanently  without calling  libPath   every time when entering in R  this works for me    create  Rprofile under your home directory      Rprofile  type   libPaths c   libPaths     your new path     in  Rprofile file  save  open R  any directory  and check  just type  libPaths    you can find your libaray path is updated

User · Answer

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   gt  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    gt   libPaths    1   C  software Rpackages                 C  Program Files R R-2 15 2 library   3   C  Program Files RStudio R library

User · Answer

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 - gt  Advanced system properties - gt  Environment Variables - gt  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  quot Open With quot  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

User · Answer

I ve had real trouble understanding this   gorkypl gave the correct solution above when I last re-installed my OS  amp  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

User · Answer

https   superuser com questions 749283 change-rstudio-library-path-at-home-directory  Edit    Renviron  R LIBS USER  some path

User · Answer

just change the default folder for your R libraries in a directory with no Administrator rights  e g    libPaths  C  R libs

User · Answer

Since most of the answers here are related to Windows  amp  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     etc R    usr lib R etc   NOTE  The Renviron config files stored at 1  amp  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

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

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