I am not sure what is causing that problem, but there is always another way to install external tools in Skyline.
You can go to the web page for that tool:
https://skyline.ms/skyts/home/software/Skyline/tools/details.view?name=AvantGardeDIA
and click the "Download AvantGardeDIA" button.
This will result in a .zip file ("AvG_skylineexternaltool_v0.0.1.5.zip") being downloaded to your computer.
Then, in Skyline, you can use the menu item:
Tools > External Tools
to bring up the "External Tools" dialog.
In the External Tools dialog you can push the "Add > From File" button and choose the .zip file that you downloaded. Skyline will then go through the process of adding the tool and installing the version of R and R packages that the tool needs.
I will try to figure out what is causing the error that you are seeing. This workaround should allow you to use the AvantGardeDIA external tool in the meantime.
-- Nick