Installing R Packages

Installing R packages

Users should install R packages for themselves locally. This documentation shows you how to install R packages locally (without root access) on Oscar.

If the package you want to install has operating-system-level dependencies (i.e. the package depends on core libraries), then we can install it as a module.

Installing an R package

First load the R version that you want to use the package with:

module load r/4.5.1

Start an R session

R

Note some packages will require code to be compiled so it is best to do R packages installs on the login node.

To install the package 'wordcloud':

> install.packages("wordcloud", repos="http://cran.r-project.org")

You will see a warning:

Warning in install.packages("wordcloud", repos = "http://cran.r-project.org") :
  'lib = "/oscar/runtime/opt/R/3.4.2/lib64/R/library"' is not writable
Would you like to use a personal library instead?  (y/n) 

Answer y . If you have not installed any R packages before you will see the following message:

Would you like to create a personal library
~/R/x86_64-pc-linux-gnu-library/3.4
to install packages into?  (y/n) 

Answer y . The package will then be installed. If the install is successful you will see a message like:

** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (wordcloud)

If the installation was not successful you will see a message like:

Warning message:
In install.packages("wordcloud", repos = "http://cran.r-project.org") :
  installation of package ‘wordcloud’ had non-zero exit status

There is normally information in the message that gives the reason why the install failed. Look for the word ERROR in the message.

Possible reasons for an installation failing include:

• Other software is needed to build the R package, e.g. the R package rgdal needs gdal so you have to do module load gdal

• A directory needs deleting from a previous failed installation.

Reinstalling R packages

To reinstall R packages, start an R session and run the update.packages() command

module load r/4.5.1
R

update.packages(checkBuilt=TRUE, ask=FALSE)

Removing an R package

Start an R session:

R

To remove the 'wordcloud' package:

> remove.packages("wordcloud")

Common Issues

libproj or sqlite3 not found in standard or given locations.

The error is reported for the sf and terre packages. To install the pakcages, run the following commands

sf

install.packages("sf", configure.args = c("--with-proj-include=/oscar/rt/9.6/25/spack/x86_64_v3/proj-9.4.1-fhhvfr6iwri5cw42roir5meojvazzfoo/include", "--with-proj-lib=/oscar/rt/9.6/25/spack/x86_64_v3/proj-9.4.1-fhhvfr6iwri5cw42roir5meojvazzfoo/lib64", "--with-sqlite3-lib=/oscar/rt/9.6/25/spack/x86_64_v3/sqlite-3.46.0-pwg7tka36sc5abuw7l637zgwrvk63tu3/lib"))

terra

install.packages("terra", configure.args = c("--with-proj-include=/oscar/rt/9.6/25/spack/x86_64_v3/proj-9.4.1-fhhvfr6iwri5cw42roir5meojvazzfoo/include", "--with-proj-lib=/oscar/rt/9.6/25/spack/x86_64_v3/proj-9.4.1-fhhvfr6iwri5cw42roir5meojvazzfoo/lib64", "--with-sqlite3-lib=/oscar/rt/9.6/25/spack/x86_64_v3/sqlite-3.46.0-pwg7tka36sc5abuw7l637zgwrvk63tu3/lib"))

The proj and sql paths need to be modified accordingly if different proj are sqlite3 modules are used.

Can not install a package in Open OnDemand (OOD) Rstudio Server app

It is recommended to install R packages from an Oscar terminal, instead of from an OOD Rstudio Server session. This is because that the Rstudio Server app runs in a container which has its own OS and system packages.