Safety, efficiency, and cleaning: Part 1 of n

[aadler]

I got a bit carried away with the size of the PR again, but now I'm testing :) This PR includes a lot of changes, all of which are documented in the commit notes. There remain files which need to be reviewed as well as some potential enhancement which this code review has uncovered, so further PRs may be forthcoming. @astamm, please let me know if you prefer more frequent but smaller-scoped PRs or fewer but larger-scoped ones such as this. Thank you.

Below is a list of most of the changes. I will try and note which of Safety, Efficiency, or Cleaning to which each relates.

• Remove CXX from Makevars per discussions here and on R-package-devel (S)
• Adjust .Call given that native registration of routines occurs so function need not be quoted and package need not be passed. (S/E)
• Based on above can now add R_forceSymbols(info, TRUE) to init (S)
• Convert citation to modern bibentry and update to what is shown on NLOPT website (E/C)
• Add more unit tests prior to changes to actual code base. Coverage now > 90% (S)
• Use "helper" variables to "cache" output of functions called on data items used > 2 times in code (E)
• Added deqn and eqn calls in nloptr help documentation for nicer output
• General code cleanup including:
  • negating functions instead of multiplying them by (-1) (specifically hin and hinjac) (E/C)
  • Replace any(is.na( with anyNA( (S/E)
  • Replace 1:length(x) with seq_along(x) where x has not already been checked for length >= 1 (S)
  • Remove unnecessary return calls when implied .Primitive(return) will suffice (E)
  • Remove unnecessary paste calls inside R message/error/warning calls (E)
  • Replace paste(., sep = "") with paste0 (E)
  • Replace = being used for assignment with <- (S)
  • Use scalar logic operators inside flow control, not vector versions (will be an error in future versions of R) (S/E)
  • Pass fixed = TRUE for grep and family when comparing to fixed string (More efficient in R-devel) (E)
  • use value = TRUE to subset grep calls instead of external explicit sub-setting along the logical (C)
  • use toString instead of paste(., collapse = ", ") (C)
  • Use double quotes (C)
  • Always place space after a comma (C)
  • Remove extra spaces between delimiters and arguments (C)
  • Add spaces between flow control operators and their tests (C)
  • Conform more often to 80 character line length when possible and not disruptive of others' work (C)
  • Replace ambiguous notice of LGPL with clear SPDX code reflecting package licensure of LGPL >= 3 (S)
  • Fix indenting especially when whitespace in parenthesis was removed (C)
  • Removed calls to c() containing only one item (E)
  • General spelling and grammar corrections (C)

[astamm]

Thanks for this PR @aadler. I am fine with large-scope PR such as this one but it is really up to you as well and to the time you have to dedicate to this. It seems all checks are successful so I am going to merge this PR unless you instruct me otherwise. Nice job, thanks a lot!