From cfa1340c41fe77117c3c2481ddbb25579f196bdd Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 30 Mar 2020 19:17:13 +0200 Subject: Don't check for gcc on the path in mkinmod Roxygen update -> formatting changes in Rd files --- R/mkinmod.R | 117 +++++++++++++++++++++++++++++------------------------------- 1 file changed, 57 insertions(+), 60 deletions(-) (limited to 'R/mkinmod.R') diff --git a/R/mkinmod.R b/R/mkinmod.R index a1ae0021..cf618525 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -364,79 +364,76 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb model$coefmat <- m }#}}} - # Try to create a function compiled from C code if more than one observed {{{ - # variable and gcc is available + # Try to create a function compiled from C code if >1 observed variable {{{ if (length(obs_vars) > 1) { - if (Sys.which("gcc") != "") { - # Translate the R code for the derivatives to C code - diffs.C <- paste(diffs, collapse = ";\n") - diffs.C <- paste0(diffs.C, ";") + # Translate the R code for the derivatives to C code + diffs.C <- paste(diffs, collapse = ";\n") + diffs.C <- paste0(diffs.C, ";") - # HS - diffs.C <- gsub(HS_decline, "(time <= tb ? k1 : k2)", diffs.C, fixed = TRUE) + # HS + diffs.C <- gsub(HS_decline, "(time <= tb ? k1 : k2)", diffs.C, fixed = TRUE) - for (i in seq_along(diffs)) { - state_var <- names(diffs)[i] + for (i in seq_along(diffs)) { + state_var <- names(diffs)[i] - # IORE - if (state_var %in% obs_vars) { - if (spec[[state_var]]$type == "IORE") { - diffs.C <- gsub(paste0(state_var, "^N_", state_var), - paste0("pow(y[", i - 1, "], N_", state_var, ")"), - diffs.C, fixed = TRUE) - } + # IORE + if (state_var %in% obs_vars) { + if (spec[[state_var]]$type == "IORE") { + diffs.C <- gsub(paste0(state_var, "^N_", state_var), + paste0("pow(y[", i - 1, "], N_", state_var, ")"), + diffs.C, fixed = TRUE) } + } - # Replace d_... terms by f[i-1] - # First line - pattern <- paste0("^d_", state_var) - replacement <- paste0("\nf[", i - 1, "]") - diffs.C <- gsub(pattern, replacement, diffs.C) - # Other lines - pattern <- paste0("\\nd_", state_var) - replacement <- paste0("\nf[", i - 1, "]") - diffs.C <- gsub(pattern, replacement, diffs.C) + # Replace d_... terms by f[i-1] + # First line + pattern <- paste0("^d_", state_var) + replacement <- paste0("\nf[", i - 1, "]") + diffs.C <- gsub(pattern, replacement, diffs.C) + # Other lines + pattern <- paste0("\\nd_", state_var) + replacement <- paste0("\nf[", i - 1, "]") + diffs.C <- gsub(pattern, replacement, diffs.C) - # Replace names of observed variables by y[i], - # making the implicit assumption that the observed variables only occur after "* " - pattern <- paste0("\\* ", state_var) - replacement <- paste0("* y[", i - 1, "]") - diffs.C <- gsub(pattern, replacement, diffs.C) - } + # Replace names of observed variables by y[i], + # making the implicit assumption that the observed variables only occur after "* " + pattern <- paste0("\\* ", state_var) + replacement <- paste0("* y[", i - 1, "]") + diffs.C <- gsub(pattern, replacement, diffs.C) + } - derivs_sig <- signature(n = "integer", t = "numeric", y = "numeric", - f = "numeric", rpar = "numeric", ipar = "integer") + derivs_sig <- signature(n = "integer", t = "numeric", y = "numeric", + f = "numeric", rpar = "numeric", ipar = "integer") - # Declare the time variable in the body of the function if it is used - derivs_code <- if (spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) { - paste0("double time = *t;\n", diffs.C) - } else { - diffs.C - } + # Declare the time variable in the body of the function if it is used + derivs_code <- if (spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) { + paste0("double time = *t;\n", diffs.C) + } else { + diffs.C + } - # Define the function initializing the parameters - npar <- length(parms) - initpar_code <- paste0( - "static double parms [", npar, "];\n", - paste0("#define ", parms, " parms[", 0:(npar - 1), "]\n", collapse = ""), - "\n", - "void initpar(void (* odeparms)(int *, double *)) {\n", - " int N = ", npar, ";\n", - " odeparms(&N, parms);\n", - "}\n\n") + # Define the function initializing the parameters + npar <- length(parms) + initpar_code <- paste0( + "static double parms [", npar, "];\n", + paste0("#define ", parms, " parms[", 0:(npar - 1), "]\n", collapse = ""), + "\n", + "void initpar(void (* odeparms)(int *, double *)) {\n", + " int N = ", npar, ";\n", + " odeparms(&N, parms);\n", + "}\n\n") - # Try to build a shared library - cf <- try(cfunction(list(func = derivs_sig), derivs_code, - otherdefs = initpar_code, - verbose = verbose, - convention = ".C", language = "C"), - silent = TRUE) + # Try to build a shared library + cf <- try(cfunction(list(func = derivs_sig), derivs_code, + otherdefs = initpar_code, + verbose = verbose, + convention = ".C", language = "C"), + silent = TRUE) - if (!inherits(cf, "try-error")) { - if (!quiet) message("Successfully compiled differential equation model from auto-generated C code.") - model$cf <- cf - } + if (!inherits(cf, "try-error")) { + if (!quiet) message("Successfully compiled differential equation model from auto-generated C code.") + model$cf <- cf } } # }}} -- cgit v1.2.1 From f9e0c46378f090a04fe95c70bb7977a686679895 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 31 Mar 2020 09:24:14 +0200 Subject: Static documentation rebuilt by pkgdown --- R/mkinmod.R | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'R/mkinmod.R') diff --git a/R/mkinmod.R b/R/mkinmod.R index cf618525..cfd40504 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -33,6 +33,7 @@ #' @param verbose If \code{TRUE}, passed to \code{\link{cfunction}} if #' applicable to give detailed information about the C function being built. #' @importFrom methods signature +#' @importFrom pkgbuild has_compiler #' @importFrom inline cfunction #' @return A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, #' containing, among others, @@ -364,8 +365,9 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb model$coefmat <- m }#}}} - # Try to create a function compiled from C code if >1 observed variable {{{ - if (length(obs_vars) > 1) { + # Try to create a function compiled from C code there is more than one observed variable {{{ + # and a compiler is available + if (length(obs_vars) > 1 & has_compiler()) { # Translate the R code for the derivatives to C code diffs.C <- paste(diffs, collapse = ";\n") -- cgit v1.2.1