Hey, thanks for getting back 
The app is running on an AWS instance with Amazon Linux, and it's standalone (no shiny server: I just run Rscript -e "shiny::runApp()" and manage the instances via pm2).
Then it's served through an haproxy instance (in this case, there's only one server in the backend).
The code is quite large, so I'm not sure what to tell you, but if you have questions in particular I'll be happy to specify.
As for permissions, yes, all seems in order (besides, the error is for a file in /tmp, which should not have any problems of that kind).
I found a reference in some Stack Exchange question, saying that the temporary file (created directly by Shiny) was deleted for some reason, but I don't see how it could happen in my case.
I think the problem happens when the app has been idling for a while (in this case, the latest log entry before the ones I posted above are from about 24 hours earlier). Does that help?