cfunction: Inline C, C++, Fortran function calls from R

Description

Functionality to dynamically define R functions and S4 methods with in-lined C, C++ or Fortran code supporting .C and .Call calling conventions.

Usage

cfunction(sig=character(), body=character(), includes=character(),
            otherdefs=character(),
            language=c("C++", "C", "Fortran", "F95", "ObjectiveC", "ObjectiveC++"),
            verbose=FALSE,
            convention=c(".Call", ".C", ".Fortran"),
            Rcpp=FALSE,
            cppargs=character(), cxxargs=character(), libargs=character(),
            dim=NULL, implicit=NULL, module=NULL, name=NULL)
  ## S4 methods for signatures
  #  f='character', sig='list', body='list'
  #  f='character', sig='character', body='character'
  setCMethod(f, sig, body, ...)
  ## Further arguments:
  #  setCMethod(f, sig, body, includes="", otherdefs="", cpp=TRUE,
  #  verbose=FALSE, where=topenv(.GlobalEnv), ...)

Arguments

A single character value if sig and body are character vectors or a character vector of the same length and the length of sig or body with the name(s) of methods to create.

sig

A match of formal argument names for the function with the character-string names of corresponding classes. Alternatively, a named list of such character vectors. The names of the list elements will be used as function names (see example). If sig is not a list, the function name used in the code can be specified by the name argument.

body

A character vector with C, C++ or Fortran code omitting function declaration (only the body, i.e. in case of C starting after the function opening curly bracket and ending before the closing curly bracket, brackets excluded). In case of setCMethod with signature list -- a list of such character vectors.

includes

A character vector of additional includes and preprocessor statements etc that will be put between the R includes and the user function(s).

otherdefs

A characted vector with the code for any further definitions of functions, classes, types, forward declarations, namespace usage clauses etc which is inserted between the includes and the declarations of the functions defined in sig.

language

A character value that specifies the source language of the inline code. The possible values for language include all those supported by R CMD SHLIB on any platform, which are currently C, C++, Fortran, F95, ObjectiveC and ObjectiveC++; they may not all be supported on your platform. One can specify the language either in full as above, or using any of the following case insensitive shortened forms: c, cpp, c++, f, f95, objc, objcpp, objc++. Defaults to C++.

verbose

If TRUE prints the compilation output, the source code of the resulting program and the definitions of all declared methods. If FALSE, the function is silent, but it prints compiler warning and error messages and the source code if compilation fails.

convention

Which calling convention to use? See the Details section.

Rcpp

If TRUE adds inclusion of Rcpp.h to includes, also queries the Rcpp package about the location of header and library files and sets environment variables PKG_CXXFLAGS and PKG_LIBS accordingly so that the R / C++ interface provided by the Rcpp package can be used. Default value is FALSE.

cppargs

Optional character vector of tokens to be passed to the compiler via the PKG_CPPFLAGS environment variable. Elements should be fully formed as for example c("-I/usr/local/lib/foo", "-DDEBUG") and are passed along verbatim.

cxxargs

Optional character vector of tokens to be passed to the compiler via the PKG_CXXFLAGS environment variable. Elements should be fully formed as for example c("-I/usr/local/lib/foo", "-DDEBUG") and are passed along verbatim.

libargs

Optional character vector of tokens to be passed to the compiler via the PKG_LIBS environment variable. Elements should be fully formed as for example c("-L/usr/local/lib/foo -lfoo", "--lpthread") and are passed along verbatim.

dim

Optional character vector defining the dimensionality of the function arguments. Of same length as sig. Fortran or F95 only.

implicit

A character vector defining the implicit declaration in Fortran or F95; the default is to use the implicit typing rules for Fortran, which is integer for names starting with the letters I through N, and real for names beginning with any other letter. As R passes double precision, this is not the best choice. Safest is to choose implicit = "none" which will require all names in the subroutine to be explicitly declared.

module

Name(s) of any modules to be used in the Fortran or F95 subroutine.

name

Function name to be used in the code. Only used if sig is not a list. This is useful if the DLL created is to be used in conjunction with the ode function of the deSolve package.

...

Reserved.

Value

If sig is a single character vector, cfunction returns a single function; if it is a list, it returns a list of functions.

setCMethod declares new methods with given names and signatures and returns invisible NULL.

Details

To declare multiple functions in the same library one can use setCMethod supplying lists of signatures and implementations. In this case, provide as many method names in f as you define methods. Avoid clashes when selecting names of the methods to declare, i.e. if you provide the same name several times you must ensure that signatures are different but can share the same generic!

The source code in the body should not include the header or "front-matter" of the function or the close, e.g. in C or C++ it must start after the C-function opening curly bracket and end before the C-function closing curly bracket, brackets should not be included. The header will be automatically generated from the R-signature argument. Arguments will will carry the same name as used in the signature, so avoid variable names that are not legal in the target language (e.g. names with dots).

C/C++: If convention == ".Call" (the default), the .Call mechanism is used and its result is returned directly as the result of the call of the generated function. As the last line of the generated C/C++ code a return R_NilValue; is added in this case and a warning is generated in case the user has forgotten to provide a return value. To suppress the warning and still return NULL, add return R_NilValue; explicitly.

Special care is needed with types, memory allocation and protection -- exactly the same as if the code was not inline: see the Writing R Extension manual for information on .Call.

If convention == ".C" or convention == ".Fortran", the .C or .Fortran mechanism respectively is used, and the return value is a list containing all arguments.

Attached R includes include R.h for ".C", and additionally Rdefines.h and R_ext\Error.h for ".Call".

Examples

Run this code

# NOT RUN {
x <- as.numeric(1:10)
n <- as.integer(10)

# }
# NOT RUN {
## A simple Fortran example - n and x: assumed-size vector
code <- "
      integer i
      do 1 i=1, n(1)
    1 x(i) = x(i)**3
"
cubefn <- cfunction(signature(n="integer", x="numeric"), code, convention=".Fortran")
print(cubefn)

cubefn(n, x)$x

## Same Fortran example - now n is one number
code2 <- "
      integer i
      do 1 i=1, n
    1 x(i) = x(i)**3
"
cubefn2 <- cfunction(signature(n="integer", x="numeric"), implicit = "none",
  dim = c("", "(*)"), code2, convention=".Fortran")

cubefn2(n, x)$x

## Same in F95, now x is fixed-size vector (length = n)
code3 <- "x = x*x*x"
cubefn3 <- cfunction(sig = signature(n="integer", x="numeric"), implicit = "none",
  dim = c("", "(n)"), code3, language="F95")
cubefn3(20, 1:20)
print(cubefn3)

## Same example in C
code4 <- "
      int i;
      for (i = 0; i < *n; i++)
        x[i] = x[i]*x[i]*x[i];
"
cubefn4 <- cfunction(signature(n="integer", x="numeric"), code4, language = "C", convention = ".C")
cubefn4(20, 1:20)

## Give the function in the source code a name
cubefn5 <- cfunction(signature(n="integer", x="numeric"), code4, language = "C", convention = ".C",
  name = "cubefn")
code(cubefn5)
# }
# NOT RUN {
 ## use of a module in F95
modct <- "module modcts
double precision, parameter :: pi = 3.14159265358979
double precision, parameter :: e = 2.71828182845905
end"

getconstants <- "x(1) = pi
x(2) = e"

cgetcts <- cfunction(getconstants, module = "modcts", implicit = "none",
  includes = modct, sig = c(x = "double"), dim = c("(2)"), language = "F95")

cgetcts(x = 1:2)
print(cgetcts)

## Use of .C convention with C code
## Defining two functions, one of which calls the other
sigSq <- signature(n="integer", x="numeric")
codeSq <- "
  for (int i=0; i < *n; i++) {
    x[i] = x[i]*x[i];
  }"
sigQd <- signature(n="integer", x="numeric")
codeQd <- "
  squarefn(n, x);
  squarefn(n, x);
"

fns <- cfunction( list(squarefn=sigSq, quadfn=sigQd),
                  list(codeSq, codeQd),
                  convention=".C")

squarefn <- fns[["squarefn"]]
quadfn <- fns[["quadfn"]]

squarefn(n, x)$x
quadfn(n, x)$x

## Alternative declaration using 'setCMethod'
setCMethod(c("squarefn", "quadfn"), list(sigSq, sigQd),
           list(codeSq, codeQd), convention=".C")

squarefn(n, x)$x
quadfn(n, x)$x

## Use of .Call convention with C code
## Multyplying each image in a stack with a 2D Gaussian at a given position
code <- "
  SEXP res;
  int nprotect = 0, nx, ny, nz, x, y;
  PROTECT(res = Rf_duplicate(a)); nprotect++;
  nx = INTEGER(GET_DIM(a))[0];
  ny = INTEGER(GET_DIM(a))[1];
  nz = INTEGER(GET_DIM(a))[2];
  double sigma2 = REAL(s)[0] * REAL(s)[0], d2 ;
  double cx = REAL(centre)[0], cy = REAL(centre)[1], *data, *rdata;
  for (int im = 0; im < nz; im++) {
    data = &(REAL(a)[im*nx*ny]); rdata = &(REAL(res)[im*nx*ny]);
    for (x = 0; x < nx; x++)
      for (y = 0; y < ny; y++) {
        d2 = (x-cx)*(x-cx) + (y-cy)*(y-cy);
        rdata[x + y*nx] = data[x + y*nx] * exp(-d2/sigma2);
      }
  }
  UNPROTECT(nprotect);
  return res;
"
funx <- cfunction(signature(a="array", s="numeric", centre="numeric"), code)

x <- array(runif(50*50), c(50,50,1))
res <- funx(a=x, s=10, centre=c(25,15))
if (interactive()) image(res[,,1])

## Same but done by registering an S4 method
setCMethod("funy", signature(a="array", s="numeric", centre="numeric"), code, verbose=TRUE)

res <- funy(x, 10, c(35,35))
if (interactive()) { x11(); image(res[,,1]) }

# }