Fix some documentation issues

[TheoPannetier]

Fixed some errors, warnings and notes I (and hopefully everyone) was getting from R check.
This is progress towards passing the CRAN check!

• explicit :: calls to packages for external functions
• fixed dependencies declared in DESCRIPTION, I just followed check's requirements there
• removing all non-ASCII UTF characters, that is mostly greek characters and replace them with corresponding LaTeX specials in equations
• removed g++-specific flags and commands in the Makevars (wildcard() and -o2)

The package builds without errors (still 3 warnings standing), but I have not attempted to run it - unsure what is the usual procedure to test the package.

[JetteReeg]

Hi Theo,
just one question: are you running R CMD check to add the GitHub Action for checking the R package?
The warnings only occur when running R CMD check, but not when users install the package from GitHub or if people would install it in RStudio. That's why we haven't had the fix as a priority. But I guess that GitHub is running R CMD check?
Regarding CRAN: we actually haven't decided yet whether RangeShiftR should be on CRAN.
I will try to look at the PR by the end of the week.

[TheoPannetier]

are you running R CMD check to add the GitHub Action for checking the R package?

Not yet, but I do indeed have this in mind! This was just because I started working on #31 and noticed the check couldn't pass on my machine because of these doc issues, so I wanted to fix part of it (and de-clutter the log) before changing anything else.

I guess that GitHub is running R CMD check?

Well since you (maintainer/dev) write the yaml script that controls what is run on GitHub Actions, what is done on GitHub is up to you :)
But I believe it is indeed standard practice to run R CMD CHECK (e.g. via the r-lib script) to ensure that your package complies with CRAN requirements through time.

we actually haven't decided yet whether RangeShiftR should be on CRAN.

Fair enough! Well if we do, this is some progress towards it.