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9.2 Lab

Exercise 1#

In this exercise you determine why a new version of R added to the server does not work with RStudio Server Pro.

Task: Install pre-compiled version of R#

Hint: Use sudo su or sudo -i to open an interactive root prompt instead of typing sudo with every command.

First, add the pre-compiled version of R to the server:

sudo cp /usr/share/class/pro_admin_training_assets/06_troubleshooting/3.0.0.tar.gz /opt/R/
cd /opt/R
sudo tar xf 3.0.0.tar.gz
ls -la

Now, restart RStudio Server for the new version of R to be detected:

sudo service rstudio-server stop
sudo service rstudio-server start

Task: Review the error log#

Do you see any errors? Review the output of:

sudo service rstudio-server status -l
sudo journalctl -u rstudio-server

Warning

You should see this error in the logs:

ERROR R shared library (/opt/R/3.0.0/lib/R/lib/libR.so) not found. 
If this is a custom build of R, was it built with the --enable-R-shlib option?

Task: Investigate#

How do you investigate this further?

Do you have permissions to access libR.so if it exists?

sudo namei -l /opt/R/3.0.0/lib/R/lib/libR.so

Does libR.so exist anywhere else?

sudo updatedb
sudo locate libR.so

Info

updatedb updates the database used by locate

What ./configure flags was this version of R compiled with? Was it built with the --enable-R-shlib option?

grep configure /opt/R/3.0.0/lib/R/etc/Makeconf

Task: Reset#

Once finished, remove the version of R and start the service:

sudo service rstudio-server stop
sudo rm -rf /opt/R/3.0.0
sudo service rstudio-server start

Exercise 2#

Task: Troubleshoot an existing R version#

Next you determine why an existing version of R on the server does not work for users anymore.

First, execute the existing_R_version script to begin the scenario:

cd /usr/share/class/pro_admin_training_assets/06_troubleshooting/
sudo chmod +x existing_R_version
sudo ./existing_R_version

Next, restart RStudio Server.

sudo service rstudio-server stop
sudo service rstudio-server start

Task: Check for errors#

Do you see any errors, when you review the output of:

sudo service rstudio-server status -l
sudo journalctl -u rstudio-server
sudo service rstudio-server stop
sudo rstudio-server verify-installation
sudo service rstudio-server start

You should observe this warning:

WARNING R version home directory not found: /opt/R/3.5.1/lib/R;

Task: Investigate#

How do you investigate this further?

  • Does the home directory exist for R 3.5.1 and are the permissions OK?
sudo ls -la /opt/R/3.5.1/lib/R
  • Was it detected by RStudio Server Pro in this internal file?
cat /var/lib/rstudio-server/r-versions

This undocumented r-versions file contains information regarding the R versions detected by RStudio Server Pro

  • Can you launch that version of R from the command line?
/opt/R/3.5.1/bin/R
  • What have you missed? Was there any command tried when troubleshooting the last R issue?

Hint: namei -l /opt/R/3.5.1/bin/R

Once you identified the issue, please correct, then restart the service.

Solution#

The permissions on /opt/R/3.5.1 were restricted to rwx by root only. This is a common oversight when installing additional versions of R. To resolve, reset permissions to allow r-x by all:

sudo chmod 755 /opt/R/3.5.1/

Exercise 3#

In this exercise, your users have reported that after logging into Rstudio Server Pro, the session crashes with an Unable to connect to service error. Maintenance was performed recently by your IT group.

Task: Simulate an R session crash#

To begin the scenario, execute the r_Session_crash script:

cd /usr/share/class/pro_admin_training_assets/06_troubleshooting/
sudo chmod +x r_Session_crash
sudo ./r_Session_crash

Are you able to reproduce the issue with your admin-user by logging into RStudio Server Pro or by starting a new session?

Task: Investigate#

How do you investigate the error, Unable to connect to service, further?

Does the rstudio-server.log contain anything relevant?

tail -n 30 /var/lib/rstudio-server/monitor/log/rstudio-server.log

What would cause an inability to find libR.so?

Does disabling the execution of the shell profiles resolve the issue? To try, edit the rserver.conf file:

Info

You can find rserver.conf at /etc/rstudio/rserver.conf

Set the value of rsession-no-profile to 1 (TRUE)

rsession-no-profile=1

Then restart the service:

service rstudio-server stop
service rstudio-server start

Are you still able to reproduce the issue with your admin-user by logging into RStudio Server Pro or by starting a new session?

Info

This option, to disable startup scripts, is a good way to troubleshoot the inability for sessions to launch, as it could indicate a conflict is occuring due to environment variables being set in the shell profiles.

To track down the source of the issue, review these common startup files:

/etc/profile
~/.bash_profile
~/.bash_login
~/.profile

Does anything appear inaccurate?

Solution#

The /etc/profile script modified the LD_LIBRARY_PATH to an invalid value.

Remember to modify the /etc/profile script to remove the invalid line and comment out rsession-no-profile=1 in your /etc/rstudio/rserver.conf file.