Earlier today the CRAN Ubuntu apt repo became corrupt due to a hardware failure of the maintainer. CRAN then sync'd the repo, which caused Release.gpg to disappear, and CRAN's repo to become corrupt. This caused the failures seen when deploying to shinyapps.io for applications that caused system dependencies to be installed.
The repositories appear to have been repaired and sync's have taken place and we have successfully tested deploying an application that had been failing. We will continue to monitor to ensure that everything has fully recovered and will discuss steps that we can take to insulate ourselves, our users and customers from such issues in the future.
We are sorry for the inconvenience this caused.