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RStudio Team System Admin :: CHEATSHEET#

Documentation#

Topic Link
General https://docs.rstudio.com/
Installing R https://docs.rstudio.com/resources/install-r/
Installing Python https://docs.rstudio.com/resources/install-python/
RStudio Server admin guide https://docs.rstudio.com/ide/server-pro/
RStudio Connect admin guide https://docs.rstudio.com/connect/admin/
RStudio Package Manager admin guide https://docs.rstudio.com/rspm/admin/
Pro Drivers https://docs.rstudio.com/pro-drivers/

Pre-requisites:

Installing R#

Install R from pre-compiled binaries#

Recommended best practise is to install R from pre-compiled binaries

https://docs.rstudio.com/resources/install-r/

For example, on Ubuntu 18.04 for R version 3.6.1.

sudo sed -i.bak "/^#.*deb-src.*universe$/s/^# //g" /etc/apt/sources.list
sudo apt-get update
sudo apt-get install gdebi-core

export R_VERSION=3.6.1

curl -O https://cdn.rstudio.com/r/ubuntu-1804/pkgs/r-${R_VERSION}_1_amd64.deb
sudo gdebi r-${R_VERSION}_1_amd64.deb

This script installs into /opt/R/...

Verify installation:

/opt/R/${R_VERSION}/bin/R --version

RStudio Server Pro#

Admin guide: https://docs.rstudio.com/ide/server-pro/

Starting, stopping and restarting#

Running the verify installation command:

sudo rstudio-server stop
sudo rstudio-server verify-installation
sudo rstudio-server start

To restart the RSP service and check its status, run these commands (with sudo if necessary):

sudo rstudio-server restart
sudo rstudio-server status

Status#

rstudio-server status

Error logs#

The locations of the various server log files:

ls /var/log/rstudio-server

cat /var/log/rstudio-server/rserver-http-error.log

The server log is at:

tail /var/lib/rstudio-server/monitor/log/rstudio-server.log

RStudio Connect#

Admin guide: https://docs.rstudio.com/connect/admin/

Config file#

/etc/rstudio-connect/rstudio-connect.gcfg

Systemd vs upstart#

Distributions using systemd include Red Hat/CentOS 7, Red Hat/CentOS 8, SUSE 12, Ubuntu 16.04, and Ubuntu 18.04.

  • systemctl start rstudio-connect

Distributions using Upstart include Red Hat/CentOS 6 and Ubuntu 14.04.

  • start rstudio-connect

Starting and stopping#

sudo systemctl start rstudio-connect
sudo systemctl stop rstudio-connect
sudo systemctl restart rstudio-connect
sudo systemctl reload rstudio-connect

Checking status#

sudo systemctl status rstudio-connect

Log files#

sudo tail /var/log/rstudio-connect.log

Get the diagnostics script#

/opt/rstudio-connect/scripts/run-diagnostics.sh

RStudio Package Manager#

Admin guide: https://docs.rstudio.com/rspm/admin/

sudo systemctl status rstudio-pm

The rspm command#

Try running the rspm command on the server instance where RSPM is installed:

/opt/rstudio-pm/bin/rspm

To save keystrokes when typing RSPM commands, create a command alias for the rspm command:

echo "alias rspm='/opt/rstudio-pm/bin/rspm'" >> ~/.bashrc

Run the rspm command with no arguments for a list of available commands:

$ rspm
Available Commands:
add          Add packages to sources
air-gap      Print help for setting up an air-gapped RStudio Package Manager service
archive      Archive packages in sources
clear-cran   Purge CRAN metadata. Cannot be used if any repos subscribe to CRAN.
create       Create entities
delete       Delete entities
edit         Edit repo name and description
fetch        Initiate eager package fetching
help         Help about any command
import       Import SSH keys
info         Print information about sources and repos
list         List entities.
logs         Retrieve logs for package builds
remove       Remove packages from sources
reorder      Reorder repo subscriptions to sources
rerun        Rerun git-builders
run          Run git-builders
subscribe    Subscribe repos to sources
sync         Initiate an ad-hoc sync of the default cran source
unsubscribe  Unsubscribe repos from sources
update       Update curated-cran sources

Working with CRAN#

sync         Initiate an ad-hoc sync of the default cran source
clear-cran   Purge CRAN metadata. Cannot be used if any repos subscribe to CRAN.

Manage repositories and sources#

create       Create entities
delete       Delete entities
list         List entities
update       Update curated-cran sources

Manage packages#

add          Add packages to sources
archive      Archive packages in sources
remove       Remove packages from sources

Working with repositories#

edit         Edit repo name and description
reorder      Reorder repo subscriptions to sources
subscribe    Subscribe repos to sources
unsubscribe  Unsubscribe repos from sources

Utilities#

air-gap      Print help for setting up an air-gapped RStudio Package Manager service
fetch        Initiate eager package fetching
help         Help about any command
import       Import SSH keys
info         Print information about sources and repos
logs         Retrieve logs for package builds

System health check#

You have various methods to check the health of your RSPM instance:

  1. View the RSPM application logs:

    sudo cat /var/log/rstudio-pm.log

  2. View the RSPM access logs:

    sudo cat /var/log/rstudio-pm.access.log

  3. Check the status of your RSPM license:

    sudo /opt/rstudio-pm/bin/license-manager status

  4. Run RSPM diagnostics:

    sudo /opt/rstudio-pm/bin/run-diagnostics

  5. View diagnostics output:

    cat rspm_diagnostics-report.txt

License manager#

View license status#

sudo /opt/rstudio-pm/bin/license-manager status

Activate license:

sudo /opt/rstudio-pm/bin/license-manager activate LICENSE_KEY

List of available commands:

sudo /opt/rstudio-pm/bin/license-manager

Supported commands: 

acquire-lease, acquire-lease-verbose, activate,
activate-offline, activate-offline-request, 
begin-evaluation-offline, ...

Expired license#

Things to try:

  • Check time and time zone timedatectl
  • Resync if needed, e.g. sudo hwclock -w
  • Restart

Deactivating a license#

Deactivation tool: http://apps.rstudio.com/deactivate-license/

Pro Drivers#

Documentation overview: https://docs.rstudio.com/pro-drivers/

Driver locations:

cat /etc/odbc.ini 
cat /etc/odbcinst.ini

Troubleshooting#

Troubleshooting R#

Almost all RStudio products depend on R being installed successfully to run.

  • Look for errors related to R in the server logs

Can R be launched manually and can the user's code be run in R without any errors?

How was R installed? 

grep configure R_HOME/etc/Makeconf

Are all necessary dependencies installed? 

apt-get build-dep r-base
yum-builddep R

Are the permissions set correctly to allow r-x by all? 

namei -l /path/to/R

Are there multiple versions of R on the system?

apt-get install mlocate
updatedb
locate libR.so

Troubleshooting configuration#

Look for any errors in the startup. You can view the live log during startup using:

tail -f /path/to/log

Read through the admin guides and make sure you have the correct formatting

Make sure you're on the right version of the product compared to the admin guide!

Troubleshooting authentication#

It is difficult for RStudio Support to troubleshoot as it depends on external configuration values unknown to us.

Does it work outside of the RStudio product?

  • Often possible to copy over working setup from other systems or services.
  • For RStudio Server Pro, thepamtester utility lets you test outside RStudio systems.
sudo /usr/lib/rstudio-server/bin/pamtester \
--verbose rstudio <username> authenticate

Check server log files including access.log files.

Check connections to any external authentication providers

  • Kerberos, Active Directory, etc.

General Linux tips#

Operating system version#

What OS are you using?

cat /etc/*-release

or

uname -a

Export environment variable to PATH#

export PATH=$PATH:/opt/R/3.5.0/bin

Persist changes on startup in .bashrc#

You can run scripts and define variables on startup by adding lines to your .bashrc file:

echo "alias rspm='/opt/rstudio-pm/bin/rspm'" >> ~/.bashrc