Installing R packages without admin access

how to

Author

Berkely Statistics

Published

July 29, 2021

How do I install R packages?

** Note that this content was copied from the Berkely Statistics Website Original article linked here

Library Path Management

First, note that in general, the administrators of the High Performance Computing clusters will install an R package on the system.

However, you can also install packages locally within your home directory. So if you need a package quickly or on a one-time basis, or if the package is particularly specialized, you might install it locally.

By default, R searches a set of paths when you request actions involving libraries. The first path is used by default when invoking functions such as install.packages() leading to messages like this:

mkdir: cannot create directory  '/server/linux/lib/R/site-library/00LOCK': Permission denied ERROR: failed to lock directory  '/server/linux/lib/R/site-library' for modifying

Fortunately, R provides a number of methods for controlling the library path to accommodate just about any user’s need.

Temporarily changing the library path

You can modify R’s notion of your library path on a one-time basis by specifying the lib= argument to install.packages. Suppose there is a directory called MyRlibs in your home directory. The command:

install.packages('caTools',lib='~/MyRlibs')

will install the specified package in your local directory. To access it, the lib.loc= argument of library must be used:

library('caTools',lib='~/MyRlibs')

One problem with this scheme is that if a local library invokes the library() function, it won’t know to also search the local library

Changing the library path for a session

The .libPaths() function accepts a character vector naming the libraries which are to be used as a search path. Note that it does not automatically retain directories which are already on the search path. Since the .libPaths() function returns the current search path when called with no arguments, a call like

.libPaths(c('~/MyRlibs',.libPaths()))

will put your local directory at the beginning of the search path. This means that install.packages() will automatically put packages there, and the library() function will find libraries in your local directory without additional arguments.

Permanently changing the library path

The environmental variable R_LIBS is set by the script that invokes R, and can be overridden (in a shell startup file, for example) to customize your library path. This variable should be set to a colon-separated string of directories to search. Since it’s always set inside of an R session, the easiest way to get a starting point for it is to use Sys.getenv():

> Sys.getenv('R_LIBS')
[1] "/usr/local/linux/lib/R/site-library:/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library"

You could then make a copy of this path, modify it, and set the R_LIBS environmental variable to that value in the shell or a startup script.

--- title: Installing R packages without admin access author: Berkely Statistics date: '2021-07-29' slug: installing-r-packages-without-admin-access categories: - how to tags: [] --- # How do I install R packages? ** Note that this content was copied from the Berkely Statistics Website [Original article linked here](https://statistics.berkeley.edu/computing/R-packages) **Library Path Management** First, note that in general, the administrators of the High Performance Computing clusters will install an R package on the system. However, you can also install packages locally within your home directory. So if you need a package quickly or on a one-time basis, or if the package is particularly specialized, you might install it locally. By default, R searches a set of paths when you request actions involving libraries. The first path is used by default when invoking functions such as `install.packages()` leading to messages like this: ``` mkdir: cannot create directory '/server/linux/lib/R/site-library/00LOCK': Permission denied ERROR: failed to lock directory '/server/linux/lib/R/site-library' for modifying ``` Fortunately, R provides a number of methods for controlling the library path to accommodate just about any user's need. ## Temporarily changing the library path You can modify R's notion of your library path on a one-time basis by specifying the `lib=` argument to `install.packages`. Suppose there is a directory called `MyRlibs` in your home directory. The command: ``` install.packages('caTools',lib='~/MyRlibs') ``` will install the specified package in your local directory. To access it, the `lib.loc=` argument of `library` must be used: ``` library('caTools',lib='~/MyRlibs') ``` One problem with this scheme is that if a local library invokes the `library()` function, it won't know to also search the local library ## Changing the library path for a session The `.libPaths()` function accepts a character vector naming the libraries which are to be used as a search path. Note that it does not automatically retain directories which are already on the search path. Since the `.libPaths()` function returns the current search path when called with no arguments, a call like ``` .libPaths(c('~/MyRlibs',.libPaths())) ``` will put your local directory at the beginning of the search path. This means that `install.packages()` will automatically put packages there, and the `library()` function will find libraries in your local directory without additional arguments. ## Permanently changing the library path The environmental variable `R_LIBS` is set by the script that invokes R, and can be overridden (in a shell startup file, for example) to customize your library path. This variable should be set to a colon-separated string of directories to search. Since it's always set inside of an R session, the easiest way to get a starting point for it is to use `Sys.getenv()`: ``` > Sys.getenv('R_LIBS') [1] "/usr/local/linux/lib/R/site-library:/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library" ``` You could then make a copy of this path, modify it, and set the `R_LIBS` environmental variable to that value in the shell or a startup script.