Rstudio

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rstudio

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On Minerva, there are two ways that you can access the rstudio interface, running Rstudio application over GUI (graphical user interface) or one simple command to get On-the-fly Rstudio over Web in a Minerva job.


Usage:

For example, to start an RStudio web session with R, on the login nodes, run commands minerva-rstudio-web-r4.sh (using R 4.0.3) or minerva-rstudio-web.sh (R 3.6.2) with default resource configuration and URL to access it. Please see the -h option for help messages containing resource requests and installing packages.


Currently, the minerva-rstudio-web-r4.sh script is the preferred version as it is built with common libraries including"DBI", "odbc", "shiny", "devtools", "ggplot2", "tidyverse", "tidymodels", "car", "dplyr", "tidyr". If you want to switch the scripts to use, move or rename the downloaded image singularity-rstudio.simg in $HOME/minerva_jobs/rstudio_jobs.

See the Package Installations section in the help message for packages not installed.






Occasionally, you may need to install an R module that requires one or more dynamic libraries from Minerva packages. In these cases, you should install the R module into the private library that is used by rstudio outside of rstudio using hard-coded paths to those libraries. The library that is automatically set up is $HOME/R/x86_64-pc-linux-gnu-library/[3.0 or 4.0].


A convenient way to signal the linker that it should encode the full path to dynamic libraries is to set LD_RUN_PATH to LD_LIBRARY_PATH after you load all the Minerva packages needed to build the R module but before you actually build the module. When you build the module, you will need to specify the destination library as the default private library for rstudio.

Example:


You will then be in and able to use R straight away. It is highly recommended you change the password immediately and an easy means of doing this is explained upon login in the script that is loaded there. However, users who are comfortable with Linux can follow the usual procedure for changing system user passwords via SSH or the Terminal tab within the RStudio interface if they prefer. Advanced users should also note that the rstudio user can use sudo.


1. Create a new GitHub repository: Login to your GitHub account and create a new GitHub repository. Give your new repository a short and memorable name e.g. rstudio-git-test, check the option to initialize this repository with a README and create the repository.


Files stored in local storage that are mounted to /home/rstudio. The home directory has a storage limitation of 2 GB and is used to store the RStudio session workspace. Note that you are allocated 2 GB for your home directory storage across all of your projects, irrespective of whether you use RStudio in each project. As a consequence, you should only store R script files and small data files in the home directory. It is not intended for large data files or large generated output. All large data files should be uploaded as project assets, which are mounted to the project-objectstorage directory from where you can access them.


To use RStudio Workbench on Databricks, you need to convert your Pro License to a floating license. For assistance, contact help rstudio.com. When your license is converted, you must set up a license server for RStudio Workbench.

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