`contrastsTest` returns NULL for all return values

[svteichman]

I believe there is a problem with the use of the function limma::makeContrasts() called by the helper function waldchisq_test() when running contrastsTest(). There are two issues that I see:

• limma has been removed from cran, and there is no error or warning when the package is not installed and the function is called, instead the function silently returns NA
• when limma is installed (it is available on Bioconductor), running `limma::makeContrasts()" results in an error about an argument not able to be found, although no error or warning is thrown and the function silently returns NA

I have currently added a warning to the contrastsTest() function that behavior is not as expected but I think this should be looked at in more detail.

[adw96]

Good catch!

If I recall correctly, statdivlab/rigr has a way to test contrasts. If we can turn a limma dependency into a rigr dependency, that would give us more control over failures.

Also, #$*& CRAN for removing all of these foundational packages!

[svteichman]

It turns out the function works for and the examples/tests for this function weren't working. They've been fixed in PR #165 so I'm closing this issue.