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RStudio

RStudio is an IDE specialized for the R programming language.

What is an IDE?

See the page on IDEs.

Using RStudio differs per UPPMAX cluster:

RStudio versions

Which versions of RStudio are available?

Use module spider Rstudio to see all versions:

[sven@r210 sven]$ module spider Rstudio

----------------------------------------------------------------------------
  RStudio:
----------------------------------------------------------------------------
     Versions:
        RStudio/1.0.136
        RStudio/1.0.143
        RStudio/1.0.153
        RStudio/1.1.423
        RStudio/1.1.463
        RStudio/1.4.1106
        RStudio/2022.02.0-443
        RStudio/2022.02.3-492
        RStudio/2022.07.1-554
        RStudio/2023.06.0-421
        RStudio/2023.06.2-561
        RStudio/2023.12.1-402 (may not always work)

Some links between version and official documentation:

RStudio module RStudio Builds documentation
RStudio/2023.06.2-561 here

Troubleshooting

RStudio runs partially

RStudio runs partially:

  • File content is displayed just fine
  • The R interpreter does not respond
  • The files pane at the bottom-right is loading forever

RStudio runs partially

In one case (see ticket for details), the problem was caused by a process called -bash (yes, the first character is a dash/minus). Killing it with kill -s 1 [PID] (for example, kill -s 1 11723) and then restarting RStudio solved the problem.

R encountered a fatal error

Full error message:

R encountered a fatal error. The session was terminated.

R encountered a fatal error. The session was terminated

This is because the home folder is full.

Check this by using uquota.md.

How does that look like?

Your output will be similar to this:

[sven@rackham3 ~]$ uquota
Your project     Your File Area       Unit        Usage  Quota Limit  Over Quota
---------------  -------------------  -------  --------  -----------  ----------
home             /home/sven           GiB          24.7           32
home             /home/sven           files       79180       300000
naiss2024-22-49  /proj/worldpeace     GiB           5.1          128
naiss2024-22-49  /proj/worldpeace     files       20276       100000

Candidates for files that are too big, that are hidden files:

  • .RData
  • .Renviron
  • .Rhistory

One can use ls -all to see all files, including hidden files:

ls --all
How does that look like?

Your output will be similar to this:

[sven@rackham2 ~]$ ls --all
.                      .gtkrc               .nextflow.log.8
..                     .ICEauthority        .nextflow.log.9
.allinea               .ipython             .nv
.bash_history          .java                .oracle_jre_usage
.bash_logout           .jupyter             .pki
.bash_profile          .kde                 private
.bashrc                .keras               .profile
.bashrc.save           .lesshst             .python_history
.beast                 lib                  .r
bin                    .lmod.d              R
.cache                 .local               .RData
.conda                 .login               .Rhistory
.config                .MathWorks           .rstudio-desktop
.cshrc                 .matlab              .ssh
.dbus                  .mozilla             .subversion
DNABERT_2              my_little_turtle.py  ticket_297538
.emacs                 .nextflow            users
.esd_auth              .nextflow.log        .viminfo
.gitconfig             .nextflow.log.1      .vscode-oss
.git-credential-cache  .nextflow.log.2      .vscode-server
glob                   .nextflow.log.3      .wget-hsts
.gnupg                 .nextflow.log.4      .Xauthority
.gracetimefile         .nextflow.log.5      .xfce4-session.verbose-log
.gradle                .nextflow.log.6      .xfce4-session.verbose-log.last
.gstreamer-0.10        .nextflow.log.7      .zshrc

You can delete these hidden files, by:

rm .RData
rm .Renviron
rm .Rhistory
For staff

Full report can be found at RT ticket 298623