Difference between revisions of "RStudio"

Latest revision as of 19:51, 18 July 2023

Description

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Environment Modules

Run module spider R to find out what R environment modules that contain this application are available.

System Variables

HPC_RSTUDIO_DIR - installation directory

Additional Information

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

The recommended way to run RStudio on HiPerGator is to start it in Open OnDemand.

When RStudio starts the file browser will be limited to your home directory. To navigate to /blue or /orange, there are two main options:

Option 1: Create a symlink to your target directory in home

E.g.

$ cd
$ ln -s /blue/MYGROUP/$USER/ blue

where MYGROUP is your real group name

After you create a symlink you'll be able to go into the 'blue' directory in the RStudio file browser under home.

Option 2: Change your working directory using R console

Click on the '[Gear] More' menu in the RStudio file browser and choose 'Synchronize Working Directory'
Run

setwd('/blue/MYGROUP/MYUSER/')

in the RStudo REPL and the file browser should immediately reflect the new working directory.

RStudio on ResVault

To launch RStudio on ResVault use the command $ rstudio --no-sandbox and if you have additional drives linked to your VM, bind mount those drives with the flag -B /drives/drive_name

@@ Line 1: / Line 1: @@
-[[Category:Software]]
+[[Category:Software]][[Category:Statistics]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|rstudio}}
@@ Line 21: / Line 21: @@
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
-===Serial===
+Run <code>module spider R</code> to find out what R environment modules that contain this application are available.
-* {{#var:app}}
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
 * HPC_{{uc:{{#var:app}}}}_DIR - installation directory
@@ Line 46: / Line 36: @@
 The recommended way to run RStudio on HiPerGator is to start it in [[Open_OnDemand|Open OnDemand]].
-Alternatively, you can use the gui module to start an interactive RStudio sessions that you can view in your web browser. See [[GUI Programs]] for more details.
+When RStudio starts the file browser will be limited to your home directory. To navigate to /blue or /orange, there are two main options:
-<pre>
+=== Option 1: Create a symlink to your target directory in home===
-[jdoe@gator ~]$ module load gui
-[jdoe@gator ~]$ gui start -e rstudio
-To load a specific version:
+E.g.
-[jdoe@gator ~]$ gui start -e rstudio --module rstudio/1.1.453
+ $ cd
+ $ ln -s /blue/MYGROUP/$USER/ blue
+where MYGROUP is your real group name
-See 'gui start -h' for arguments to specify a resource request and so on.
+After you create a symlink you'll be able to go into the 'blue' directory in the RStudio file browser under home.
-;Note:
+===Option 2: Change your working directory using R console===
-:If you see your mouse cursor offset from the real location in the RStudio window check your RStudio editor font preferences. A known good font is 'DejaVu Sans Mono'.
+* Click on the '[Gear] More' menu in the RStudio file browser and choose 'Synchronize Working Directory'
+* Run
+ setwd('/blue/MYGROUP/MYUSER/')
+in the RStudo REPL and the file browser should immediately reflect the new working directory.
+[[File:RStudio setwd synchronize.png]]
 |}}
+==RStudio on ResVault==
+To launch RStudio on ResVault use the command <code>$ rstudio --no-sandbox</code> and if you have additional drives linked to your VM, bind mount those drives with the flag <code> -B /drives/drive_name</code>
 <!--Job Scripts-->
 {{#if: {{#var: job}}|==Job Script Examples==