Thank you so much for the reference to milla! It is a lifesaver!

So for anyone who was wondering when I was using PAUSE I was using the upload a url option. Using a git I created a branch for each version (like the git workflow best practices recommends) and was using the URL to that branch.

I think that what happened is that it needs to be an archive, tar or zip. So if I had used https://github.com/jerowe/Annovar-Wrapper/archive/Annovar-Wrapper-1.1.zip maybe that would have been ok, but just giving PAUSE https://github.com/jerowe/Annovar-Wrapper/tree/Annovar-Wrapper-1.1 did not work. As it turns out the PAUSE upload form says archives only, but I thought that it had a utility for git since I saw that referenced.

I'm going to just use milla, but its nice to know how to do it both ways. ;) A big thanks to everyone for your help!