When working on a unix system, the ~ expands my directory to my unix home. When on my windows computer, I would like ~ to expand to the drive that is mapped and points to the Unix home. I am using RStudio for coding on the windows computer and it expands the ~ to something that isn't helpful and I am having trouble changing it. I have played with the environment variables and PATH but cannot get it to point to what I want. Any ideas?
UPDATE:
Per Josh's answer. Changing the R_USER environment variable in windows, prior to starting RStudio yields on startup:
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'rstudio' was found
Changing it manually every time after RStudio startup is possible using this answer but I would like to avoid doing that.
To change the value of ~ from its default, you need to set R_USER before your first call to path.expand() et al. (This is documented in ?path.expand.)
Try this:
## R
Sys.getenv("R_USER")
# [1] "C:\\Users\\Josh"
Sys.setenv(R_USER="C://")
path.expand("~")
# [1] "C://"
To set the starting value of "R_USER" for all of your R/Rstudio sessions, just add a line like the following to your ~/.Renviron or $R_HOME/etc/Renviron.site or wherever you prefer. (As always, see ?Startup for the full set of options.):
R_USER = "C:/"
What is your .libPaths() after starting RStudio? I note that if I start RStudio on Windows without setting R_USER, I get:
> .libPaths()
[1] "C:/Users/Kevin/Documents/R/win-library/3.1"
[2] "C:/Program Files/R/R-3.1.0/library
The first library path is automatically generated by RStudio, and it installs rstudio and manipulate packages there automatically on startup (because it may not have permissions to write to the default, 'system' library).
However, if R_USER is set, then that library path is not set, and this appears to cause problems with the installation of these packages.
I believe you should be able to work around this by also setting the R_LIBS_USER environment variable accordingly -- it should be set to somewhere that RStudio has permissions to write to. See ?libPaths for more information on how that might be appropriately set.
Consider using ${} in Renviron.site to call Windows environment variables. To make R_USER point to each user's document folder, you can put the following in Renviron.site:
R_USER=C:/Users/${USERNAME}/Documents
I have a similar situation and for my needs it was easiest to redefine the HOME-parameter with the line below:
Sys.setenv(HOME="path/to/desired/tilde-folder/")
path.expand("~") # Check that it worked.
Update: Just realised that this solution does not appear to work on my Windows machine, only on a Linux server I was using.
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.
Asked on superuser and got crickets, so trying here. This one seems to straddle the border of SU/SO.
In troubleshooting some kind of R configuration issue that was causing a pandoc conversion failure when trying to Knit a .Rmd on a colleague's Windows 10 machine, I noticed that the first path in .libPaths() was pointing to a path on a network directory rather than the c:/Users/[username]/R/win-library/... directory.
Running Sys.getenv() in R showed that HOMEDRIVE and HOMEPATH were (as expected) c: and \Users\[username], yet there was a HOME environment variable listed that was pointing to the network path that we'd found in .libPaths()
Running SET in a cmd shell did not list this HOME environment variable at all, so it seems to be something that R found somewhere else...
Where does R get this HOME environment variable?
FWIW: I fixed the config issue by setting a Windows User Environment variable HOME=%HOMEDRIVE%%HOMEPATH%; R then set all the other environment variables appropriately from there.
R startup is somewhat complicated, but it is pretty well documented. The usual starting place is help("Startup"). The answer to your question is not documented there, but you will find this clue in the See also section:
For the definition of the ‘home’ directory on Windows see the ‘rw-FAQ’
Q2.14. It can be found from a running R by Sys.getenv("R_USER")
and indeed the cited FAQ at https://cran.r-project.org/bin/windows/base/rw-FAQ.html#What-are-HOME-and-working-directories_003f gives us the answer:
The home directory is set as follows: If environment variable R_USER
is set, its value is used. Otherwise if environment variable HOME is
set, its value is used. After those two user-controllable settings, R
tries to find system-defined home directories. It first tries to use
the Windows "personal" directory (typically
C:\Users\username\Documents). If that fails, if both environment
variables HOMEDRIVE and HOMEPATH are set (and they normally are), the
value is ${HOMEDRIVE}${HOMEPATH}. If all of these fail, the current
working directory is used.
You might want to take a look at the here package and, relating to knitr, the ezknitr package. Also, in RStudio, you can specify in the knit menu if the knitting will happen in the current dir, working dir or project dir, as shown here.
Update: let me reiterate the message here since it got downvoted: in a typical usage scenario you don't have to modify the HOME environment variable. Using a proper workflow (e.g. RStudio projects or the here package) is a more robust and portable solution.
The tilde expression is not working on my RStudio! I am using a windows 10 OS.
Update : After looking more carefully(thanks to Dason) It seems the "~" is pointing to "user/Documents/" rather then "user/". is there any work around?
Any help?
The home directory in Windows R is set using the environment variable R_USER Set this using Windows (search from the Start Menu for "environment variable"). Whatever you set this to will become what R uses for ~. I have mine set to C:\Users\trehman\R.
Here is how mine looks.
As you found out yourself, R's ~ points to your documents folder. An easy way to work around this could be to start the paths you want to reference with ~/../. So your setwd call would look like this:
setwd('~/../{your actual path from home}')
The same problem occurs on my Windows PC. I do not have a Linux machine at hand to test whether it is the same there. R gets this variable from the R_USER environment variable. You can override that in your R environment startup file. This issue is not specific to RStudio and also occurs when you start an R session from the command line.
At startup, R looks for Renviron.site in the R_HOME directory. Open and edit it
file.edit(file.path(Sys.getenv('R_HOME'), 'etc', 'Renviron.site'))
Define R_USER in that file with the path you want '~' to point to:
R_USER = 'C:/Users/USERNAME'
References:
R for Enterprise: Understanding R’s Startup
I have attempted to install R and R studio on the local drive on my work computer as opposed to the organization network folder because anything that runs through the network is really slow. When installing, the destination path shows that it's my local C:drive. However, when I install a new package, the default path shown is my network drive and there is no option to change:
.libPaths()
[1] "\\\\The library/path/I/don't/want"
[2] "C:/Program Files/R/R-3.2.1/library"
I'm running windows 7 professional. How can I remove library path [1] and make path [2] my primary for all base packages and all new packages that I install?
Windows 7/10: If your C:\Program Files (or wherever R is installed) is blocked for writing, as mine is, then you'll get frustrated editing RProfile.site (as I did). As specified in the accepted answer, I updated R_LIBS_USER and it worked. However, even after reading the fine manual several times and extensive searching, it took me several hours to do this. In the spirit of saving someone else time...
Let's assume you want your packages to reside in C:\R\Library:
Create the folder C:\R\Library. Next I need to add this folder to the R_LIBS_USER path:
Click Start --> Control Panel --> User Accounts --> Change my environmental variables
The Environmental Variables window pops up. If you see R_LIBS_USER, highlight it and click Edit. Otherwise click New. Both actions open a window with fields for Variable and Value.
In my case, R_LIBS_USER was already there, and Value was a path to my desktop. I added to the path the folder that I created, separated by semicolon. C:\R\Library;C:\Users\Eric.Krantz\Desktop\R stuff\Packages.
(NOTE: In the last step, I could have removed the path to the Desktop location and simply left C:\R\Library).
See help(Startup) and help(.libPaths) as you have several possibilities where this may have gotten set. Among them are
setting R_LIBS_USER
assigning .libPaths() in .Rprofile or Rprofile.site
and more.
In this particular case you need to go backwards and unset whereever \\\\The library/path/I/don't/want is set.
To otherwise ignore it you need to override it use explicitly i.e. via
library("somePackage", lib.loc=.libPaths()[-1])
when loading a package.
Facing the very same problem (avoiding the default path in a network) I came up to this solution with the hints given in other answers.
The solution is editing the Rprofile file to overwrite the variable R_LIBS_USER which by default points to the home directory.
Here the steps:
Create the target destination folder for the libraries, e.g.,
~\target.
Find the Rprofile file. In my case it was at C:\Program Files\R\R-3.3.3\library\base\R\Rprofile.
Edit the file and change the definition the variable R_LIBS_USER. In my case, I replaced the this line file.path(Sys.getenv("R_USER"), "R", with file.path("~\target", "R",.
The documentation that support this solution is here
Original file with:
if(!nzchar(Sys.getenv("R_LIBS_USER")))
Sys.setenv(R_LIBS_USER=
file.path(Sys.getenv("R_USER"), "R",
"win-library",
paste(R.version$major,
sub("\\..*$", "", R.version$minor),
sep=".")
))
Modified file:
if(!nzchar(Sys.getenv("R_LIBS_USER")))
Sys.setenv(R_LIBS_USER=
file.path("~\target", "R",
"win-library",
paste(R.version$major,
sub("\\..*$", "", R.version$minor),
sep=".")
))
Windows 10 on a Network
Having your packages stored on the network drive can slow down the performance of R / R Studio considerably, and you spend a lot of time waiting for the libraries to load/install, due to the bottlenecks of having to retrieve and push data over the server back to your local host. See the following for instructions on how to create an .RProfile on your local machine:
Create a directory called C:\Users\xxxxxx\Documents\R\3.4 (or whatever R version you are using, and where you will store your local R packages- your directory location may be different than mine)
On R Console, type Sys.getenv("HOME") to get your home directory (this is where your .RProfile will be stored and R will always check there for packages- and this is on the network if packages are stored there)
Create a file called .Rprofile and place it in :\YOUR\HOME\DIRECTORY\ON_NETWORK (the directory you get after typing Sys.getenv("HOME") in R Console)
File contents of .Rprofile should be like this:
#search 2 places for packages- install new packages to first directory- load built-in packages from the second (this is from your base R package- will be different for some)
.libPaths(c("C:\Users\xxxxxx\Documents\R\3.4", "C:/Program Files/Microsoft/R Client/R_SERVER/library"))
message("*** Setting libPath to local hard drive ***")
#insert a sleep command at line 12 of the unpackPkgZip function. So, just after the package is unzipped.
trace(utils:::unpackPkgZip, quote(Sys.sleep(2)), at=12L, print=TRUE)
message("*** Add 2 second delay when installing packages, to accommodate virus scanner for R 3.4 (fixed in R 3.5+)***")
# fix problem with tcltk for sqldf package: https://github.com/ggrothendieck/sqldf#problem-involvling-tcltk
options(gsubfn.engine = "R")
message("*** Successfully loaded .Rprofile ***")
Restart R Studio and verify that you see that the messages above are displayed.
Now you can enjoy faster performance of your application on local host, vs. storing the packages on the network and slowing everything down.
I was struggling for a while with this as my work computer (with Windows 10) created the default user library on a network drive, which would slow down R and RStudio to an unusable state.
In case this helps someone, this is the easiest way I found, without requiring admin rights:
make sure the directory you want to install your packages into exists. If you want to respect the convention, use: C:\Users\username\R\win-library\rversion (for example, something like: C:\Users\janebloggs\R\win-library\3.6)
create a .Renviron file in your home directory (which might be on the network drive?), and in it, write one single line that defines the R_LIBS_USER variable to be your custom path:
R_LIBS_USER=C:\Users\janebloggs\R\win-library\3.6
(feel free to add comments too, with lines starting with #)
If a .Renviron file exists, R will read it at startup and use the variables as they are defined in there, before running the code in the .Rprofile. You can read about it in help(Startup).
Now it should be persistent between sessions!
After a couple of hours of trying to solve the issue in several ways, some of which are described here, for me (on Win 10) the option of creating a Renviron file worked, but a little different from what was written here above.
The task is to change the value of the variable R_LIBS_USER. To do this two steps needed:
Create the file named Renviron (without dot) in the folder \Program\etc\ (Program is the directory where R is installed--for example, for me it was C:\Program Files\R\R-4.0.0\etc)
Insert a line in Renviron with new path: R_LIBS_USER = "C:/R/Library"
After that, reboot R and use .libPaths() to confirm the default directory changed.
I think I tried all of the above and it didn't work for me. This worked, though:
In home directory, make a file called ".Renviron"
In that file, write:
.libPaths(new = "/my/path/to/libs")
Save and restart R if you had it open
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.