First of all, thank you for bearing with us in this delay. Historically new versions of R were made available for Ubuntu on CRAN just a few days after the regular release, and we were caught flat-footed; our apologies.
In order to support R 3.5.0 and to have more control in the future, on 5/31/2018 we will be updating the base system that we provide on shinyapps.io from Ubuntu 14.04 (trusty) to Ubuntu 16.04 (xenial). Initially only new applications and new deployments of existing applications will take advantage of this. If you run into any issues while deploying your application after this change, please reach out to us (here, or at email@example.com if you are on paid plan) and we will be happy to assist.
As an additional benefit of this change, the issues with the tensorflow and keras packages that surfaced when pip 10 was released also appear to have been resolved.
Thank you again for your patience,
The shinyapps.io team