Unfortunately this post is closed without solution due to inactivity (@rstudio, please keep such posts open longer!). We had the same issue and I would like to post our solution.
In our case f-secure was running which prevented installation, even though we were running as root.
We first stopped the f-secure services
sudo service fsaua stop
sudo service fsma stop
after that the command
sudo gdebi rstudio-server-pro-1.1.463-amd64.deb
ran as expected