Problem
I have a conda environment with an R installation. My issue is that the conda R will run ~/.Rprofile during startup. This is breaking the expectation that conda environments are self-contained. Specifically, I am loading packages in my ~/.Rprofile that are not installed in the conda R (I am using require(), so just warnings). The process works the following way:
The first .Rprofile file found on the R startup search path is processed. The search path is (in order): (i) Sys.getenv("R_PROFILE_USER"), (ii) ./.Rprofile, and (iii) ~/.Rprofile. Source: startup package vignette
Goal
Ideally, I would like to alter the third path to a location within the environment directory and somehow do this in the environment yaml during setup, such that I can easily replicate the setup on another device. I realize that this might not work, so a solution that permanently sets R_PROFILE_USER to an environment-specific location would also be appreciated.
Edit:
Since I am using R through rpy2 I don't think I can use the --no-init-file flag.
Quoting from ?.Rprofile, which invokes the man page for Startup,
unless --no-init-file was given, R searches for a user profile, a file
of R code. The path of this file can be specified by the
R_PROFILE_USER environment variable (and tilde expansion will be
performed). If this is unset, a file called ‘.Rprofile’ is searched
for in the current directory or in the user's home directory (in that
order). The user profile file is sourced into the workspace.
I wrote a bash script to solve this issue. Run it in the project directory containing the environment.yml. It prompts for a name of the newly created conda environment, then creates and activates it. Subsequently an empty .Rprofile is created in the environment directory and R_PROFILE_USER is set to this location. Finally, the environment is reactivated for the change to take effect. Thus, any time R is run from this environment, the newly created .Rprofile is used.
It should be noted that an .Rprofile in R_PROFILE_USER takes precedence over an .Rprofile in the project directory. This might lead to confusion if the user wants to create use such a file and is unaware of the setup.
echo What name do you want to give to the conda environment?
read input
conda env create -n $input -f environment.yml
conda activate $input
touch $CONDA_PREFIX/.Rprofile
conda env config vars set R_PROFILE_USER=$CONDA_PREFIX
conda activate $input
Related
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?
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:
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" > .Renviron Make sure the spelling and 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.
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
just change the default folder for your R libraries in a directory with no Administrator rights, e.g.
.libPaths("C:/R/libs")
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
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.
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.
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
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
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!
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:
/etc/R/
/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 !!
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
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.
After seeing this post on how to set the start-up folder for Jupyter Notebooks, I looked for how to do so for specific conda environments and haven't found an answer.
Is there a way to open up a Jupyter notebook in a location that is different depending on which conda environment within which you're activating it? I'm looking for a solution like the one above, where I could change c.NotebookApp.notebook_dir = '/the/path/to/home/folder/', but in some environment-specific config file.
I guess an alternative would be to set some macro to activate the environment, cd to the desired folder location for this environment, then run jupyter notebook from that location.
I was able to generate a DOSKEY macro to do the job. I combined this answer which shows how to set persistent aliases (macros) in command prompt, with this answer which shows how to use multiple separate commands in a DOSKEY macro. As a summary here (mostly from Argyll's answer in the above persistent macro/DOSKEY post):
Create a file called something like alias.cmd
Insert the macro to automatically activate a conda environment, change file locations, and run a jupyter notebook from that location:
doskey start_myEnv = conda activate myEnv $T cd C:\Users\user\path\to\my\notebooks\ $T jupyter notebook
Run regedit and go to HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Command Processor
or HKEY_CURRENT_USER\Software\Microsoft\Command Processor if not on Windows 10.
Add a String entry with the name AutoRun with the value set as the full path to the alias.cmd file.
Anytime you open the command prompt, executing start_myEnv will now activate myEnv, change to the folder that relates to that environment, and start a jupyter notebook.
I'm writing a Git hook which should run some R code. If the hook starts with
#!/usr/bin/env Rscript
then the following code is correctly interpreted as R.
However, Rscript looks for my installed packages in my home directory. According to the R for Windows FAQ, the home directory is defined by the environment variables R_USER or HOME. However, the Git Bash shell does not contain either of these, so the home directory defaults to the working directory.
The hook, therefore, fails to locate any non-base packages.
The solution I've found is to create an R file and then use Bash in the hook to call Rscript after manually defining R_USER:
#!/bin/sh
R_USER="my/home/directory"
export R_USER
Rscript foo.R
(Where foo.R is in the project's working directory, in this case).
This works but is somewhat inelegant. I'd rather simply use Rscript in the hook itself.
So I considered setting the home directory within the Rscript:
#!/usr/bin/env Rscript
Sys.setenv(R_USER = "my/home/directory")
But while that does set R_USER, it doesn't fix the problem. I assume this means that R defines the package-finding path before the script itself is run, so defining R_USER within the script doesn't change the fact that it's still looking for packages in the working directory instead.
So, is there a solution to this (for example, by setting R_USER and then somehow telling R to update the package directory)? Or is the use-Bash-to-call-Rscript method the way to go?
I am trying to run R scripts via BAT files on Windows Command Prompt.
The scripts require a few R packages such as data.table, tidyR, etc.
For operational reasons, all required R packages and dependencies (including data.table) are installed at C:\Users\username\Documents\R\R-3.5.1\library. I am not allowed to install RStudio in this environment.
When I try
"C:\Program Files\R\R-3.5.1\bin\x64\Rscript.exe" script.R, I get an error similar to
Error in library(data.table) : there is no package called 'data.table'
Execution halted
How can I set the .libPaths via Command Prompt to point to the correct location of the packages (i.e. to C:\Users\username\Documents\R\R-3.5.1\library)?
Thank you in advance.
Disclaimer: I'm unfamiliar with R.
From R: Search paths :
The library search path is initialized at startup from the environment
variable R_LIBS (which should be a colon-separated list of directories
at which R library trees are rooted) followed by those in environment
variable R_LIBS_USER. Only directories which exist at the time will be
included.
By default R_LIBS is unset, and R_LIBS_USER is set to directory
‘R/R.version$platform-library/x.y’ of the home directory (or
‘Library/R/x.y/library’ for CRAN macOS builds), for R x.y.z.
An environment variable can be created with set VARIABLE_NAME=YOUR_VALUE batch command.
So your batch file should probably be something like this:
cd /d "C:\INSERT_PATH_TO_DIRECTORY_CONTAINING_script.R"
set "R_LIBS=C:\Users\username\Documents\R\R-3.5.1\library"
"C:\Program Files\R\R-3.5.1\bin\x64\Rscript.exe" script.R
However for portability reasons (let's say a collegue asks for a copy of your script or your computer dies) I suggest putting the script, R library and batch file in a single directory, let's say C:\Users\username\Documents\R. The batch file C:\Users\username\Documents\R\script.bat becomes:
cd /d "%~dp0"
set "R_LIBS=%~dp0R-3.5.1\library"
"%PROGRAMFILES%\R\R-3.5.1\bin\x64\Rscript.exe" "%~dpn0.R"
%PROGRAMFILES% environment variable expands to full path of program files folder, %~dp0 parameter expands to full path of a directory that holds your batch file, and %~dpn0 is a batch-file full path without extension.
Notice that %~dp0R-3.5.1 is not a typo because %~dp0 includes trailing backslash.
This way you can copy C:\Users\username\Documents\R to D:\Users\SOMEOTHERNAME\Documents\R and the script will still run.
If you create another version of your script, just copy the batch file so that it has same filename as your script but .bat extension instead of .R and it should call the new script - this has proven to be very handy when debugging and distributing scripts.
Alternatively, if you would rather install libraries separately you may want to use %HOMEDRIVE%%HOMEPATH% which expands to C:\Users\username.
Extracting proper Documents folder path, as well as R installation path is possible but requires reading the registry and thus is a bit more complicated.
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?
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:
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" > .Renviron Make sure the spelling and 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.
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
just change the default folder for your R libraries in a directory with no Administrator rights, e.g.
.libPaths("C:/R/libs")
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
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.
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.
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
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
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!
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:
/etc/R/
/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 !!
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
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.