chore(groupComparisonPTM): Fix bugs and unit tests

[tonywu1999]

Motivation and Context

Problem 1

This commit is causing build failures.

Problem 2

User was having issues because proteinGroups was NULL when including a global proteome dataset. User should get an error about this field being null. Right now, the error is:

Error in data.table::fread(input, showProgress = FALSE, ...) : 
  input= must be a single character string containing a file name, a system command containing at least one space, a URL starting 'http[s]://', 'ftp[s]://' or 'file://', or, the input data itself containing at least one \n or \r

Changes

• Fix changes related to groupComparisonPTM in code and tests
• Add error message early on that validates that the proteinGroups file is not null

Testing

Dry run passes

Checklist Before Requesting a Review

• I have read the MSstats contributing guidelines
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules