Chapter 9 R coding standards

R is meant to run on a wide variety of platforms, including Linux and most variants of Unix as well as Windows and macOS. Therefore, when extending R by either adding to the R base distribution or by providing an add-on package, one should not rely on features specific to only a few supported platforms, if this can be avoided. In particular, although most R developers use GNU tools, they should not employ the GNU extensions to standard tools. Whereas some other software packages explicitly rely on e.g. GNU make or the GNU C++ compiler, R does not. Nevertheless, R is a GNU project, and the spirit of the GNU Coding Standards should be followed if possible.

The following tools can “safely be assumed” for R extensions.

  • An ISO C99 C compiler. Note that extensions such as POSIX 1003.1 must be tested for, typically using Autoconf unless you are sure they are supported on all mainstream R platforms (including Windows and macOS).
  • A FORTRAN 77 compiler (but not Fortran 9x, although it is nowadays widely available).

  • A simple make, considering the features of make in 4.2 BSD systems as a baseline.

    GNU or other extensions, including pattern rules using ‘%’, the automatic variable ‘$^’, the ‘+=’ syntax to append to the value of a variable, the (“safe”) inclusion of makefiles with no error, conditional execution, and many more, must not be used (see Chapter “Features” in the GNU Make Manual for more information). On the other hand, building R in a separate directory (not containing the sources) should work provided that make supports the VPATH mechanism.

    Windows-specific makefiles can assume GNU make 3.79 or later, as no other make is viable on that platform.

  • A Bourne shell and the “traditional” Unix programming tools, including grep, sed, and awk.

    There are POSIX standards for these tools, but these may not be fully supported. Baseline features could be determined from a book such as The UNIX Programming Environment by Brian W. Kernighan & Rob Pike. Note in particular that ‘|’ in a regexp is an extended regexp, and is not supported by all versions of grep or sed. The Open Group Base Specifications, Issue 7, which are technically identical to IEEE Std 1003.1 (POSIX), 2008, are available at http://pubs.opengroup.org/onlinepubs/9699919799/mindex.html.

Under Windows, most users will not have these tools installed, and you should not require their presence for the operation of your package. However, users who install your package from source will have them, as they can be assumed to have followed the instructions in “the Windows toolset” appendix of the “R Installation and Administration” manual to obtain them. Redirection cannot be assumed to be available via system as this does not use a standard shell (let alone a Bourne shell).

In addition, the following tools are needed for certain tasks.

  • Perl version 5 is only needed for a few uncommonly-used tools: make install-info needs Perl installed if there is no command install-info on the system, and for the maintainer-only script tools/help2man.pl.
  • Makeinfo version 4.7 or later is needed to build the Info files for the R manuals written in the GNU Texinfo system.

It is also important that code is written in a way that allows others to understand it. This is particularly helpful for fixing problems, and includes using self-descriptive variable names, commenting the code, and also formatting it properly. The R Core Team recommends to use a basic indentation of 4 for R and C (and most likely also Perl) code, and 2 for documentation in Rd format. Emacs (21 or later) users can implement this indentation style by putting the following in one of their startup files, and using customization to set the c-default-style to “bsd” and c-basic-offset to 4.) 

;;; ESS
(add-hook 'ess-mode-hook
          (lambda ()
            (ess-set-style 'C++ 'quiet)
            ;; Because
            ;;                                 DEF GNU BSD K&R C++
            ;; ess-indent-level                  2   2   8   5   4
            ;; ess-continued-statement-offset    2   2   8   5   4
            ;; ess-brace-offset                  0   0  -8  -5  -4
            ;; ess-arg-function-offset           2   4   0   0   0
            ;; ess-expression-offset             4   2   8   5   4
            ;; ess-else-offset                   0   0   0   0   0
            ;; ess-close-brace-offset            0   0   0   0   0
            (add-hook 'local-write-file-hooks
                      (lambda ()
                        (ess-nuke-trailing-whitespace)))))
(setq ess-nuke-trailing-whitespace-p 'ask)
;; or even
;; (setq ess-nuke-trailing-whitespace-p t)
;;; Perl
(add-hook 'perl-mode-hook
          (lambda () (setq perl-indent-level 4)))

(The ‘GNU’ styles for Emacs’ C and R modes use a basic indentation of 2, which has been determined not to display the structure clearly enough when using narrow fonts.)