How to update to specific R version on Linux (Red Hat/CentOS), keeping the previous version?

Question

Perhaps a more accurate title would be: "How to switch from in-place (EPEL) R to side-by-side (version-specific) R installation on Linux (Red Hat/CentOS)?

A (possibly typical) upgrading R on Linux story...

History:

At some point in the past, I updated the version of R on our RHEL/CentOS 7 server using the default version pulled down by the yum package manager at that time. For example, sudo yum install R to version 3.5.2 at some point in early 2019. By default, this installs R at /usr/lib64/R for all users and completely replaces the 3.4.x version that had previously been installed there. Shiny Server was already installed, configured to run as user shiny , and it picked up the new version of R without a hitch.

Situation:

A year later, it is now time to bite the bullet and update the version of R that is running on the Linux server. Running yum check-upgrade R I find that the version available is 3.6.0. I actually want to install 3.6.3 AND I don't want to break all of my apps that are running on 3.5.2, so I need to use a different method. Following the instructions found at https://docs.rstudio.com/resources/install-r/ , I download the 3.6.3.rpm file and install it. By default, this installs R at /opt/R/3.6.3/ , leaving the 3.5.2 version as is. However, as soon as I complete the Create a symlink to R step, none of my shiny apps work:

sudo ln -s /opt/R/3.6.3/bin/R /usr/local/bin/R  
sudo ln -s /opt/R/3.6.3/bin/Rscript /usr/local/bin/Rscript  

This should not be surprising. My shiny apps all rely upon several R packages that have not yet been installed for this new version of R. I can quickly get my apps working again on the previous version (3.5.2) by removing these symlinks until after I've installed the necessary packages in the new version:

sudo rm /usr/local/bin/R  
sudo rm /usr/local/bin/Rscript 

Error messages in my shiny app log files (at /var/log/shiny-server/<app name>-<user>-<datetime>.log ) confirm that the apps had failed to launch due to missing packages. To update the R packages in the shared library folder, I need to run the new version of R as sudo: sudo -i /opt/R/3.6.3/bin/R and install the necessary packages, eg, install.packages(c("shiny","devtools","rmarkdown","shinydashboard","tidyverse")) in R.

Now that the R packages are installed, I can re-create the symlinks:

sudo ln -s /opt/R/3.6.3/bin/R /usr/local/bin/R  
sudo ln -s /opt/R/3.6.3/bin/Rscript /usr/local/bin/Rscript  

I verify that my apps are working with the new version of R.

Now I have some questions:

Question 1: After completing these steps, R --version still returns the old version (3.5.2). But when I logged back in the following day, it opens 3.6.3. Why? Do I need to run a terminal command to get R --version to return the new version immediately or is opening a new terminal window the only way to achieve this?

Question 2: Running sudo R --version always returns the old version (3.5.2). Running sudo which R returns /bin/R . Running more /bin/R reveals contents which state that it is "Shell wrapper for R executable." and has the "/usr/lib64/R" path hard-coded. I don't think I need this wrapper at this point. What is the recommended way to get these sudo commands to point to the new version?

I can make a backup copy of this file in my home directory (eg, cp /bin/R ~/binR.backup ) just in case, and then:

• Delete /bin/R?
• Replace /bin/R with a symlink to the new version (eg, sudo ln -s /opt/R/3.6.3/bin/R /bin/R )?
• Re-install the 'old' version into /opt/R/3.5.2/ using a.rpm the same way I installed 3.6.3, install packages there, and then remove the /usr/lib64/R version (eg, sudo yum remove R )?

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Links to similar questions that I looked at but didn't answer my questions:

1. How to upgrade R in Linux
2. Change path in Linux
3. How can I load a specific version of R in Linux

Answer 1

Question 1: I'm not sure why, but having multiple versions of R on your PATH can lead to unexpected situations like this. /usr/local/bin is usually ahead of /usr/bin in the PATH, so I would've expected R 3.6.3 to be found. Perhaps it has to do with Question 2.

Question 2: Some distros (like CentOS/RHEL) don't put /usr/local/bin on the PATH by default when using sudo. See https://unix.stackexchange.com/questions/8646/why-are-path-variables-different-when-running-via-sudo-and-su for details. The answers there describe several ways to add /usr/local/bin to the PATH when using sudo -- for example, modifying secure_path in /etc/sudoers to include /usr/local/bin like:

Defaults    secure_path = /usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin

With R 3.6.3 ahead of the default system R in the PATH, you shouldn't have to delete /bin/R or /usr/bin/R . But eventually, I'd recommend installing multiple side-by-side versions of R the same way, using https://docs.rstudio.com/resources/install-r/ , so it's easier to manage. The next time you install a new R version, you can just replace the symlinks in /usr/local/bin . The default system R (from EPEL) is meant to be the only R on a system, with in-place upgrades.

If you want to replace the default R 3.5.2 with a side-by-side R 3.5.2 (or 3.5.3), you could install R 3.5 from https://docs.rstudio.com/resources/install-r/ , install all necessary packages, and have Shiny Server use the new R 3.5. Then uninstall the R from EPEL ( R-core or R-core-devel ) to fully switch over. From there, you could even create symlinks to R in /usr/bin instead of /usr/local/bin , and not worry about adding /usr/local/bin to the sudo PATH.