Chapter 2 .Internal vs .Primitive

C code compiled into R at build time can be called directly in what are termed primitives or via the .Internal interface, which is very similar to the .External interface except in syntax. More precisely, R maintains a table of R function names and corresponding C functions to call, which by convention all start with ‘do_’ and return a SEXP. This table (R_FunTab in file src/main/names.c) also specifies how many arguments to a function are required or allowed, whether or not the arguments are to be evaluated before calling, and whether the function is ‘internal’ in the sense that it must be accessed via the .Internal interface, or directly accessible in which case it is printed in R as .Primitive.

Functions using .Internal() wrapped in a closure are in general preferred as this ensures standard handling of named and default arguments. For example, grep is defined as

grep <-
function (pattern, x, = FALSE, perl = FALSE, value = FALSE,
         fixed = FALSE, useBytes = FALSE, invert = FALSE)
    if (!is.character(x)) x <- structure(as.character(x), names = names(x))
    .Internal(grep(as.character(pattern), x,, value,
                   perl, fixed, useBytes, invert))

and the use of as.character allows methods to be dispatched (for example, for factors).

However, for reasons of convenience and also efficiency (as there is some overhead in using the .Internal interface wrapped in a function closure), the primitive functions are exceptions that can be accessed directly. And of course, primitive functions are needed for basic operations—for example .Internal is itself a primitive. Note that primitive functions make no use of R code, and hence are very different from the usual interpreted functions. In particular, formals and body return NULL for such objects, and argument matching can be handled differently. For some primitives (including call, switch, .C and .subset) positional matching is important to avoid partial matching of the first argument.

The list of primitive functions is subject to change; currently, it includes the following.

  1. “Special functions” which really are language elements, but implemented as primitive functions:
    {       (         if     for      while  repeat  break  next
    return  function  quote  switch
  2. Language elements and basic operators (i.e., functions usually not called as foo(a, b, …)) for subsetting, assignment, arithmetic, comparison and logic:

                   [    [[    $    @
    <-   <<-  =    [<-  [[<-  $<-  @<-
    +    -    *    /     ^    %%   %*%  %/%
    <    <=   ==   !=    >=   >
    |    ||   &    &&    !

    When the arithmetic, comparison and logical operators are called as functions, any argument names are discarded so positional matching is used.

  3. “Low level” 0– and 1–argument functions which belong to one of the following groups of functions:
    1. Basic mathematical functions with a single argument, i.e.,

      abs     sign    sqrt
      floor   ceiling
      exp     expm1
      log2    log10   log1p
      cos     sin     tan
      acos    asin    atan
      cosh    sinh    tanh
      acosh   asinh   atanh
      cospi   sinpi   tanpi
      gamma   lgamma  digamma trigamma
      cumsum  cumprod cummax  cummin
      Im  Re  Arg  Conj  Mod

      log is a primitive function of one or two arguments with named argument matching.

      trunc is a difficult case: it is a primitive that can have one or more arguments: the default method handled in the primitive has only one.

    2. Functions rarely used outside of “programming” (i.e., mostly used inside other functions), such as
      nargs          missing        on.exit        interactive        as.character   as.complex     as.double
      as.environment as.integer     as.logical     as.raw
      is.array       is.atomic        is.character
      is.complex     is.double      is.environment is.expression
      is.finite      is.function    is.infinite    is.integer
      is.language    is.list        is.logical     is.matrix        is.nan         is.null
      is.numeric     is.object      is.pairlist    is.raw
      is.real        is.recursive   is.single      is.symbol
      baseenv        emptyenv       globalenv
      unclass        invisible      seq_along      seq_len
    3. The programming and session management utilities
      browser  proc.time  gc.time tracemem retracemem untracemem
  4. The following basic replacement and extractor functions

    length      length<-
    class       class<-
    oldClass    oldCLass<-
    attr        attr<-
    attributes  attributes<-
    names       names<-
    dim         dim<-
    dimnames    dimnames<-

    Note that optimizing NAMED = 1 is only effective within a primitive (as the closure wrapper of a .Internal will set NAMED = 2 when the promise to the argument is evaluated) and hence replacement functions should where possible be primitive to avoid copying (at least in their default methods).

  5. The following functions are primitive for efficiency reasons:

    :          ~          c           list
    call       expression substitute
    UseMethod  standardGeneric
    .C         .Fortran   .Call       .External
    round      signif      rep

    as well as the following internal-use-only functions

    .Primitive     .Internal
    .subset        .subset2
    .primTrace     .primUntrace

The multi-argument primitives

call       switch
.C         .Fortran   .Call       .External

intentionally use positional matching, and need to do so to avoid partial matching to their first argument. They do check that the first argument is unnamed or for the first two, partially matches the formal argument name. On the other hand,

attr       attr<-     browser     rememtrace substitute  UseMethod
log        round      signif      rep

manage their own argument matching and do work in the standard way.

All the one-argument primitives check that if they are called with a named argument that this (partially) matches the name given in the documentation: this is also done for replacement functions with one argument plus value.

The net effect is that argument matching for primitives intended for end-user use as functions is done in the same way as for interpreted functions except for the six exceptions where positional matching is required.

2.1 Special primitives

A small number of primitives are specials rather than builtins, that is they are entered with unevaluated arguments. This is clearly necessary for the language constructs and the assignment operators, as well as for && and || which conditionally evaluate their second argument, and ~, .Internal, call, expression, missing, on.exit, quote and substitute which do not evaluate some of their arguments.

rep and are special as they evaluate some of their arguments conditional on which are non-missing.

log, round and signif are special to allow default values to be given to missing arguments.

The subsetting, subassignment and @ operators are all special. (For both extraction and replacement forms, $ and @ take a symbol argument, and [ and [[ allow missing arguments.)

UseMethod is special to avoid the additional contexts added to calls to builtins.

2.2 Special internals

There are also special .Internal functions: NextMethod, Recall, withVisible, cbind, rbind (to allow for the deparse.level argument), eapply, lapply and vapply.

2.3 Prototypes for primitives

Prototypes are available for the primitive functions and operators, and these are used for printing, args and package checking (e.g. by tools::checkS3methods and by package codetools). There are two environments in the base package (and namespace), ‘.GenericArgsEnv’ for those primitives which are internal S3 generics, and ‘.ArgsEnv’ for the rest. Those environments contain closures with the same names as the primitives, formal arguments derived (manually) from the help pages, a body which is a suitable call to UseMethod or NULL and environment the base namespace.

The C code for print.default and args uses the closures in these environments in preference to the definitions in base (as primitives).

The QC function undoc checks that all the functions prototyped in these environments are currently primitive, and that the primitives not included are better thought of as language elements (at the time of writing

$  $<-  &&  (  :  @  @<-  [  [[  [[<-  [<-  {  ||  ~  <-  <<-  =
break  for function  if  next  repeat  return  while

). One could argue about ~, but it is known to the parser and has semantics quite unlike a normal function. And : is documented with different argument names in its two meanings.

The QC functions codoc and checkS3methods also make use of these environments (effectively placing them in front of base in the search path), and hence the formals of the functions they contain are checked against the help pages by codoc. However, there are two problems with the generic primitives. The first is that many of the operators are part of the S3 group generic Ops and that defines their arguments to be e1 and e2: although it would be very unusual, an operator could be called as e.g. “+”(e1=a, e2=b) and if method dispatch occurred to a closure, there would be an argument name mismatch. So the definitions in environment .GenericArgsEnv have to use argument names e1 and e2 even though the traditional documentation is in terms of x and y: codoc makes the appropriate adjustment via tools:::.make_S3_primitive_generic_env. The second discrepancy is with the Math group generics, where the group generic is defined with argument list (x, …), but most of the members only allow one argument when used as the default method (and round and signif allow two as default methods): again fix-ups are used.

Those primitives which are in .GenericArgsEnv are checked (via tests/primitives.R) to be generic via defining methods for them, and a check is made that the remaining primitives are probably not generic, by setting a method and checking it is not dispatched to (but this can fail for other reasons). However, there is no certain way to know that if other .Internal or primitive functions are not internally generic except by reading the source code.

2.4 Adding a primitive

[For R-core use: reverse this procedure to remove a primitive. Most commonly this is done by changing a .Internal to a primitive or vice versa.]

Primitives are listed in the table R_FunTab in src/main/names.c: primitives have ‘Y = 0’ in the ‘eval’ field.

There needs to be an ‘\alias’ entry in a help file in the base package, and the primitive needs to be added to one of the lists at the start of this section.

Some primitives are regarded as language elements (the current ones are listed above). These need to be added to two lists of exceptions, langElts in undoc() (in file src/library/tools/R/QC.R) and lang_elements in tests/primitives.R.

All other primitives are regarded as functions and should be listed in one of the environments defined in src/library/base/R/zzz.R, either .ArgsEnv or .GenericArgsEnv: internal generics also need to be listed in the character vector .S3PrimitiveGenerics. Note too the discussion about argument matching above: if you add a primitive function with more than one argument by converting a .Internal you need to add argument matching to the C code, and for those with a single argument, add argument-name checking.

Do ensure that make check-devel has been run: that tests most of these requirements.