My coworker and I use the same .Rmd file to produce a flexdashboard. She has slightly older versions of some packages which I can't get to match up. When I run the dashboard, the output is perfect on my personal machine and I can send it to others and it works fine. When I upload it to our company site, the file is not able to be loaded.
Specifically, I get these errors:

I believe that this is because of the
<script src="data:application/javascript;base64
that are in my code.
When my coworker runs the same code, here's the output (which is without the encoding):
<script>/*! jQuery v1.12.4 | (c) jQuery Foundation | jquery.org/license */
!function(a,b){"object"==typeof module&&"object"==typeof module.exports?
Can someone please help me with what settings I can change in order to get the more raw output instead?