Nothing
#--------------------------------------------------
# .C2funcaddresses
# Purpose:
# takes in a C file or C scripts
# returns a list of addresses of the compiled model functions and maybe R functions for debug purposes
#------------------------------------------------
# Changed DLL name and directory to be user-specified and permanent
.C2funcaddress<-function(verbose,isContinuousTime, infile, outfile,compileLib){
#-------Set some variables: This function may later be extended----------
language <- "C"
#-------Get the full name of the library----------
if ( .Platform$OS.type == "windows" ) outfile <- gsub("\\\\", "/", outfile)
libLFile <- paste(outfile, .Platform$dynlib.ext, sep="")
if (compileLib|(!file.exists(libLFile))){#when the compileLib flag is TRUE or when the libLFile does not exist
#-------Check the input arguments----------------------------
code <- readLines(infile)
# ---- Write and compile the code ----
print("Get ready!!!!")
#filename<- basename(tempfile())
CompileCode(code, language, verbose, libLFile)
#---- SET A FINALIZER TO PERFORM CLEANUP: register an R function to be called upon garbage collection of object or at the end of an R session---
#cleanup <- function(env) {
# if ( filename %in% names(getLoadedDLLs()) ) dyn.unload(libLFile)
# unlink(libLFile)
# }
#reg.finalizer(environment(), cleanup, onexit=TRUE)
}
#-----dynamically load the library-------
DLL <- dyn.load( libLFile )
if (isContinuousTime){
res <- list(f_measure=getNativeSymbolInfo("function_measurement", DLL)$address,
f_dx_dt=getNativeSymbolInfo("function_dx_dt", DLL)$address,
f_dF_dx=getNativeSymbolInfo("function_dF_dx", DLL)$address,
f_dP_dt=getNativeSymbolInfo("function_dP_dt", DLL)$address,
f_initial_condition=getNativeSymbolInfo("function_initial_condition", DLL)$address,
f_regime_switch=getNativeSymbolInfo("function_regime_switch", DLL)$address,
f_noise_cov=getNativeSymbolInfo("function_noise_cov", DLL)$address,
f_transform=getNativeSymbolInfo("function_transform", DLL)$address)
}else{
res <- list(f_measure=getNativeSymbolInfo("function_measurement", DLL)$address,
f_dynamic=getNativeSymbolInfo("function_dynam", DLL)$address,
f_jacob_dynamic=getNativeSymbolInfo("function_jacob_dynam", DLL)$address,
f_initial_condition=getNativeSymbolInfo("function_initial_condition", DLL)$address,
f_regime_switch=getNativeSymbolInfo("function_regime_switch", DLL)$address,
f_noise_cov=getNativeSymbolInfo("function_noise_cov", DLL)$address,
f_transform=getNativeSymbolInfo("function_transform", DLL)$address)
}
return(list(address=res, libname=libLFile))
}
#--------------------------------------------------
# CompileCode: A function adapted from the compileCode function in the inline pacakge
# Purpose: compiles a C file to create a shared library
#------------------------------------------------
CompileCode <- function(code, language, verbose, libLFile) {
wd <- getwd()
on.exit(setwd(wd))
## Prepare temp file names
if ( .Platform$OS.type == "windows" ) {
## windows files
#outfile <- gsub("\\\\", "/", outfile)
## windows gsl flags
LIB_GSL <- Sys.getenv("LIB_GSL")
LIB_GSL <- gsub("\\\\", "/", LIB_GSL) # replace "\" with "/"
LIB_GSL <- gsub("\"", "", LIB_GSL) # remove "
gsl_cflags <- sprintf( "-I\"%s/include\"", LIB_GSL)
gsl_libs <- sprintf( "-L\"%s/lib/%s\" -lgsl -lgslcblas", LIB_GSL, .Platform$r_arch)
}else {
## UNIX-alike build
## Unix gsl flags
gsl_cflags <- system( "gsl-config --cflags" , intern = TRUE )
gsl_libs <- system( "gsl-config --libs" , intern = TRUE )
# Perhaps change above to use similar to configure.win syntax
# GSL_CFLAGS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "RcppGSL:::CFlags()"`
# GSL_LIBS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "RcppGSL:::LdFlags()"`
}
if (verbose) cat("Setting PKG_CPPFLAGS to", gsl_cflags, "\n")
Sys.setenv(PKG_CPPFLAGS=gsl_cflags)
if (verbose) cat("Setting PKG_LIBS to", gsl_libs, "\n")
Sys.setenv(PKG_LIBS=gsl_libs)
#libCFile <- paste(outfile, ".EXT", sep="")
libCFile <-sub(.Platform$dynlib.ext,".EXT",libLFile)
extension <- switch(language, "C++"=".cpp", C=".c", Fortran=".f", F95=".f95",
ObjectiveC=".m", "ObjectiveC++"=".mm")
libCFile <- sub(".EXT$", extension, libCFile)
#libLFile <- paste(outfile, .Platform$dynlib.ext, sep="")
## Write the code to the temp file for compilation
write(code, libCFile)
## Compile the code using the running version of R if several available
#if ( file.exists(libLFile) ) {file.remove( libLFile )}
setwd(dirname(libCFile))
errfile <- paste( basename(libCFile), ".err.txt", sep = "" )
cmd <- paste(R.home(component="bin"), "/R CMD SHLIB ", basename(libCFile), " ", gsl_libs, " ", " 2> ", errfile, sep="")
if (verbose) cat("Compilation argument:\n", cmd, "\n")
compiled <- system2(paste0(R.home(component="bin"), "/R"),
args=c("CMD", "SHLIB", basename(libCFile)),
stderr=errfile, stdout=verbose)
errmsg <- readLines(errfile)
unlink(errfile)
#if(length(errmsg) > 0){cat("May I present to you your error messages?\n")}
writeLines(errmsg)
setwd(wd)
#### Error Messages
#cat("I got here!!!")
errmsg = errmsg[!grep("warning",errmsg)]
if ( !file.exists(libLFile) | length(errmsg) > 0 ) {
cat("\nERROR(s) during compilation: source code errors or compiler configuration errors!\n")
cat("\nProgram source:\n")
codeWithLineNums <- paste(sprintf(fmt="%3d: ", 1:length(code)), code, sep="")
writeLines(codeWithLineNums)
stop("Compilation ERROR, function(s)/method(s) not created!")
}
#return( libLFile )
}
#------------------------------------------------------------------------------
# Check configuration
##' Check that dynr in configured properly
##'
##' @param verbose logical. Whether to print messages during/after checks
##'
##' @details
##' The 'dynr' package requires additional set-up and configuration beyond
##' just installing the package. In particular, it requires compiling C code
##' along with GSL to run (cook) models. This function runs some basic checks
##' of the configuration. We check that (1) R is on the PATH variable, (2)
##' Rtools exists and is on the PATH variable for Windows, (3) a C compiler
##' is available, and (4) GSL is available and on the PATH.
##'
##' In general, see the 'Installation for Users' vignette for set-up and
##' configuration instructions.
##'
##' @return No return value.
##'
##' @examples
##' \dontrun{dynr.config()}
dynr.config <- function(verbose=FALSE){
genmsg <- paste0(
"\nPlease read the 'Installation for Users' vignette at\n",
"https://cran.r-project.org/web/packages/dynr/",
"vignettes/InstallationForUsers.pdf",
"\nor\n",
"vignette(package='dynr', 'InstallationForUsers')\n")
# Check that R is on the path
noRmsg <- "R did not appear to be on the 'PATH' environment variable."
# Check that Rtools exists and is on the path
noRtoolsmsg <- "No Rtools found in 'PATH' environment variable."
# Check for a C compiler
noCmsg <- "No C compiler found."
# Check for GSL
noGSLmsg <- "LIB_GSL variable not found."
if ( .Platform$OS.type == "windows" ) {
path <- Sys.getenv("PATH")
path <- normalizePath(strsplit(path, split=';', fixed=TRUE)[[1]])
path <- gsub("\\\\", "/", path)
path <- paste(path, sep='', collapse=';')
rpath <- normalizePath(R.home(component="bin"))
rpath <- gsub("\\\\", "/", rpath)
findR <- grep(rpath, path)
if(length(findR) < 1 || findR != 1){
# Only warning
# R does NOT need to be on the path for windows unless you're a developer
warning(paste0(noRmsg, '\nThis is only needed for developers.\nIf that is not you, then happily ignore this warning.\n'))
}
if(grep('rtools', path, ignore.case=TRUE) != 1){
stop(paste0(noRtoolsmsg, genmsg))
}
if(!checkForCompiler() ){
stop(paste0(noCmsg, genmsg))
}
## windows gsl flags
LIB_GSL <- Sys.getenv("LIB_GSL")
LIB_GSL <- gsub("\\\\", "/", LIB_GSL) # replace "\" with "/"
LIB_GSL <- gsub("\"", "", LIB_GSL) # remove "
if(nchar(LIB_GSL) < 1){
stop(paste0(noGSLmsg, genmsg))
}
}else {
## UNIX-alike build
if(!checkForCompiler() ){
stop(paste0(noCmsg, genmsg))
}
## Unix gsl flags
# Wrap system command in try
# If try error, say can't find gsl
gsl_cflags <- try(system( "gsl-config --cflags", intern=TRUE), silent=TRUE)
if(inherits(gsl_cflags, 'try-error')){
stop("'gsl-config --cflags' failed. You probably need to install GSL and/or add it to your path.")
}
gsl_libs <- try(system( "gsl-config --libs", intern=TRUE), silent=TRUE)
if(inherits(gsl_cflags, 'try-error')){
stop("'gsl-config --libs' failed. You probably need to install GSL and/or add it to your path.")
}
# Sys.setenv(PATH=paste0(Sys.getenv("PATH"),":","/opt/local/bin"))
}
if(verbose){
message("Configuration check complete. Ready to rock and roll.")
}
}
# Taken from Rcpp
checkForCompiler <- function(minVersion = package_version("4.6.0")){
binaries <- c("g++", Sys.getenv("CXX", unset = ""),
Sys.getenv("CXX1X", unset = ""))
binpaths <- lapply(binaries, function(b) {
if (b == "")
NULL
else Sys.which(b)
})
allgood <- FALSE
rl <- lapply(binpaths, function(b) {
if (is.null(b))
return(NULL)
con <- pipe(paste(b, "-v 2>&1"), "r")
lines <- readLines(con)
close(con)
lines <- lines[grepl("^g.. version", lines)]
if (length(lines) == 0)
return(NULL)
ver <- strsplit(lines, " ")[[1]][3]
package_version(ver) >= minVersion
})
all(do.call(c, rl))
}
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