Tests failing on all platforms

[gtollefson]

Bug Description

Tests fail on all platforms. See test logs for details. One error on each platform, windows error looks ggplot2 related. Mac and Unix look related to deprecated read file function.

Expected Behavior

Tests should pass

Required Action

Debug each

[arisp99]

I just pushed a series of commits, which should help with test failures. There are still several tests that fail for various reasons, but I have made some progress so far. The remaining test failures are mainly the result of changes in dependencies and deprecated functions/arguments/usages.