Package 'inline'

Title: Functions to Inline C, C++, Fortran Function Calls from R
Description: Functionality to dynamically define R functions and S4 methods with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling conventions.
Authors: Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel, Romain Francois, Karline Soetaert, Johannes Ranke
Maintainer: Dirk Eddelbuettel <[email protected]>
License: LGPL
Version: 0.3.19.1
Built: 2024-05-19 17:19:52 UTC
Source: https://github.com/eddelbuettel/inline

Help Index


Functions to Inline C, C++, Fortran Function Calls from R

Description

Functionality to dynamically define R functions and S4 methods with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling conventions.

Maintainer

Dirk Eddelbuettel <[email protected]>

Author(s)

Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel, Romain Francois, Karline Soetaert, Johannes Ranke

See Also

cfunction, cxxfunction


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

f

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.

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".

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.

Author(s)

Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel

See Also

Foreign Function Interface

Examples

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)

## End(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]) }

inline C++ function

Description

Functionality to dynamically define an R function with inlined C++ code using the .Call calling convention.

The rcpp() wrapper sets the plugin to the “Rcpp” value suitable for using Rcpp.

Usage

cxxfunction(sig = character(), body = character(), 
            plugin = "default", includes = "", 
            settings = getPlugin(plugin), ..., verbose = FALSE)
rcpp(..., plugin="Rcpp")

Arguments

sig

Signature of the function. A named character vector

body

A character vector with C++ code to include in the body of the compiled C++ function

plugin

Name of the plugin to use. See getPlugin for details about plugins.

includes

User includes, inserted after the includes provided by the plugin.

settings

Result of the call to the plugin

...

Further arguments to the plugin

verbose

verbose output

Value

A function

See Also

cfunction

Examples

## Not run: 
# default plugin
fx <- cxxfunction(signature(x = "integer", y = "numeric"), 
	          "return ScalarReal(INTEGER(x)[0] * REAL(y)[0]);")
fx(2L, 5)

# Rcpp plugin
if (requireNamespace("Rcpp", quietly=TRUE)) {

    fx <- cxxfunction(signature(x = "integer", y = "numeric"), 
                      "return wrap( as<int>(x) * as<double>(y));",
                      plugin = "Rcpp" )
    fx(2L, 5)

    ## equivalent shorter form using rcpp()
    fx <- rcpp(signature(x = "integer", y = "numeric"),
               "return wrap(as<int>(x) * as<double>(y));")
}

# RcppArmadillo plugin
if (requireNamespace(RcppArmadillo)) {
	
    fx <- cxxfunction(signature(x = "integer", y = "numeric"),
                      "int dim = as<int>(x);
		       arma::mat z = as<double>(y) * arma::eye<arma::mat>(dim, dim);
		       return wrap(arma::accu(z));",
                      plugin = "RcppArmadillo")
    fx(2L, 5)
}

## End(Not run)

Retrieve the dynamic library (or DLL) associated with a package of a function generated by cfunction

Description

The getDynLib function retrieves the dynamic library (or DLL) associated with a package or with a function generated by cfunction

Methods

signature(x = "CFunc")

Retrieves the dynamic library associated with the function generated by cfunction. The library is dynamically loaded if necessary.

signature(x = "CFuncList")

Retrieves the dynamic library associated with a set of functions generated by cfunction. The library is dynamically loaded if necessary.

signature(x = "character")

Retrieves the dynamic library of the given name. This typically refers to package names, but can be any name of the list returned by getLoadedDLLs

See Also

getLoadedDLLs, dyn.load

Examples

## Not run: 
getDynLib( "base" )

f <- cfunction( signature() , "return R_NilValue ;" )
getDynLib( f )


## End(Not run)

Generate the skeleton of a package

Description

Generate the skeleton of a package

Methods

signature(name = "ANY", list = "ANY")

Standard method. See package.skeleton

signature(name = "character", list = "CFunc")

Method for a single generated by cfunction or cxxfunction

signature(name = "character", list = "CFuncList")

Method for a set functions generated by cfunction or cxxfunction

Examples

## Not run: 

fx <- cxxfunction(signature(x = "integer", y = "numeric"),
	          "return ScalarReal( INTEGER(x)[0] * REAL(y)[0]);")
package.skeleton("foo", fx)

functions <- cxxfunction(list(ff = signature(), 
                              gg = signature(x = "integer", y = "numeric")), 
                         c("return R_NilValue ;",
                           "return ScalarReal(INTEGER(x)[0] * REAL(y)[0]);"))
package.skeleton("foobar", functions)


## End(Not run)

Plugin system for cxxfunction

Description

cxxfunction uses a plugin system to assembly the code that it compiles. These functions allow to register and get plugins by their name.

Usage

getPlugin(name, ...)
registerPlugin(name, plugin)

Arguments

name

name of the plugin.

...

Further argments to pass to the plugin.

plugin

plugin function.

Details

plugins are functions that return a list with :

includes

mandatory. it is included at the top of the compiled file by cxxfunction

body

optional. a function that takes one argument (the body of the c++ function) and returned a modified version of the body. The "Rcpp" plugin uses this to surround the code with the BEGIN_RCPP and END_RCPP macros

LinkingTo

optional. character vector containing the list of packages that the code needs to link to. This adds the include path of the given packages. The "Rcpp" and "RcppArmadillo" plugins use this.

env

optional. named list of environment variables. For example, the "Rcpp" plugin uses this to add Rcpp user library to the PKG_LIBS environment variable.

plugins can be manually registered using the registerPlugin function. Alternatively, a package may supply an inline plugin implicitely by defining a function called inlineCxxPlugin, which does not necessarily need to be exported from the namespace of the package.

Known packages implementing this scheme include Rcpp and RcppArmadillo.

Value

getPlugin retrieves the plugin and invokes it with the ... arguments

registerPlugin does not return anything.

See Also

cxxfunction

Examples

## Not run: 
getPlugin( "Rcpp" )

## End(Not run)

Printing, reading and writing compiled function objects

Description

moveDLL moves the DLL used by a compiled function to a user defined location.

writeCFunc saves a CFunc object after the DLL has been moved to the desired location using moveDLL.

readCFunc reads a CFunc object that has been saved using writeCFunc.

The print and code methods respectively print the entire object or only the code parts.

Usage

moveDLL(x, ...)
## S4 method for signature 'CFunc'
moveDLL(x, name, directory, unload = FALSE, overwrite = FALSE, verbose = FALSE)

writeCFunc(x, file)
readCFunc(file)

## S4 method for signature 'CFunc'
print(x)
## S4 method for signature 'CFuncList'
print(x)

## S4 method for signature 'CFunc'
code(x, linenumbers = TRUE)
## S4 method for signature 'CFuncList'
code(x, linenumbers = TRUE)

Arguments

x

A CFunc or CFuncList object as created by cfunction

name

The base of the file name that the DLL should be moved to. The file name extension will depend on the operating system used

directory

The directory that the DLL should be written to

unload

In case the new path constructed from name and directory points to a loaded DLL, should we unload it?

overwrite

In case there is a file at the new path constructed from name and directory should we overwrite that file?

verbose

Should we print a message stating where the DLL was copied if the operation was successful?

file

The file path for writing and reading the object generated by cfunction. Consider using a file name extension like .rda or .RData to indicate that this is a serialized R object.

linenumbers

If TRUE all code lines will be numbered.

...

May be used in future methods

Details

If you move the DLL to a user defined location with moveDLL, this will keep an on-disk copy of the DLL which will prevent it from being lost at session termination - unless written to the session tempdir. Saving and reloading the CFunc object with standard tools like save or saveRDS will still loose the pointer to the DLL. However, when the DLL has been moved using moveDLL, CFunc objects can be saved by writeCFunc and restored by readCFunc.

Value

Function readDynLib returns a CFunc object.

Function writeDynLib returns the name of the .CFunc file that was created.

Note

  • The code of a CFunc or CFuncList object x can be extracted (rather than printed), using:

    x@code.

  • To write the code to a file (here called "fn"), without the new-line character "\n":

    write (strsplit(x, "\n")[[1]], file = "fn")

Author(s)

Karline Soetaert and Johannes Ranke

See Also

getDynLib

Examples

x <- as.numeric(1:10)
n <- as.integer(10)

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")
code(cubefn)

cubefn(n, x)$x

## Not run: 
# The following code is exempted from the automated tests of example code, as
# it writes to the users home directory.
# The following writes the DLL, e.g. cubefn.so on Linux/Unix or cubefn.dll
# on Windows
moveDLL(cubefn, name = "cubefn", directory = "~")
path <- file.path("~", "cubefn.rda")
writeCFunc(cubefn, path)
rm(cubefn)

# Now you can start a fresh R session and load the function
library(inline)
path <- file.path("~", "cubefn.rda")
cfn <- readCFunc(path)
cfn(3, 1:3)$x

## End(Not run)