If you updated your shiny-server version however old version of shiny-server config is not cleaned up above issue will occur. in order to overcome the issue remove the old shiny-server package and re-install it.
Or
install newer version them existing so old version config will auto cleanup by new version.
# systemctl stop shiny-server.service
# systemctl status shiny-server.service
# yum remove shiny-server
Loaded plugins: fastestmirror, langpacks
Examining shiny-server-1.5.9.923-x86_64.rpm: shiny-server-1.5.9.923-1.x86_64
Marking shiny-server-1.5.9.923-x86_64.rpm as an update to shiny-server-1.4.2.786-1.x86_64
Resolving Dependencies
--> Running transaction check
---> Package shiny-server.x86_64 0:1.4.2.786-1 will be updated
---> Package shiny-server.x86_64 0:1.5.9.923-1 will be an update
--> Finished Dependency Resolution
Dependencies Resolved
=====================================================================================================================================
Package Arch Version Repository Size
=====================================================================================================================================
Updating:
shiny-server x86_64 1.5.9.923-1 /shiny-server-1.5.9.923-x86_64 229 M
Transaction Summary
=======================================================================================================================================
Upgrade 1 Package
Total size: 229 M
Is this ok [y/d/N]: y
Downloading packages:
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
Updating : shiny-server-1.5.9.923-1.x86_64 1/2
User shiny already exists. Ensuring proper permissions on /home/shiny/.
Cleanup : shiny-server-1.4.2.786-1.x86_64 2/2
Verifying : shiny-server-1.5.9.923-1.x86_64 1/2
Verifying : shiny-server-1.4.2.786-1.x86_64 2/2
Updated:
shiny-server.x86_64 0:1.5.9.923-1
Complete!
# systemctl restart shiny-server
# systemctl status shiny-server
● shiny-server.service - ShinyServer