I just tried this on a computer that I did not have admin access on, and I was able to successfully install the MSstats external tool in Skyline.
A user does not need to be an administrator to install R.
When you ask Skyline to install the MSstats external tool, Skyline first looks in the registry to see whether R version 3.5.0 is already installed. The two places that Skyline looks in the registry are:
and if Skyline does not find anything there, it looks in:
If Skyline does not find that R is installed there, then Skyline launches the R installer. I believe you do not need to be an administrator to install R. On the last page of the R installer, there is a checkbox "Save version number in the registry" and it's very important that you leave that checked, since otherwise Skyline will never know that R is installed.
After I successfully installed R, I did get a prompt which asked me to provide an administrator password. I just pushed the "No" button on that dialog, and then Skyline went on with the rest of the process which is to install all of the R packages that MSstats needs and then add the MSstats menu items to Skyline's Tools menu.
I recommend that you try one of the following:
1. This user logs in with their regular account and tries to install the MSstats external tool in Skyline. If any prompts come up asking to provide administrator credentials they press no.
If that does not work then try:
2. An administrator installs R version 3.5.0. After that, the user logs in with their regular account and tries to install the MSstats external tool in Skyline.
Or, maybe try:
3. The user tries to install the MSstats external tool in Skyline, and then provides administrator credentials when prompted.
When you install an external tool in Skyline, the new menu items get stored in the per-user Skyline settings. For this reason, if you were to log in as someone else and install an external tool, the user would not see that when they run Skyline.
I should also mention that we have an installer for Skyline that does allow you to specify an installation folder. However, installing external tools for users with that installation is much more difficult (I do not know how to do it). This is called the "Administrator Installer" which you can download here:
I hope this helps.