
R Under development (unstable) (2026-05-06 r90009 ucrt) -- "Unsuffered Consequences"
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> ## This is only for rxode2
> for (f in c("inst/include/rxode2_RcppExports.h", "src/RcppExports.cpp")) {
+   l <- readLines(f)
+   w <- which(regexpr("^[#]include <RcppArmadillo.h>", l) != -1)
+   if (length(w) > 0) {
+     l <- l[-w]
+   }
+   w <- which(regexpr("^[#]define R_STRICT_HEADERS", l) != -1)
+   if (length(w) > 0) {
+     l <- l[-w]
+   }
+   l <- c("#define R_STRICT_HEADERS",
+          "#include <RcppArmadillo.h>",
+          l)
+   file.out <- file(f, "wb")
+   writeLines(l, file.out)
+   close(file.out)
+ }
> 
> l <- readLines("R/RcppExports.R")
> w <- which(regexpr("# Register entry points", l, fixed=TRUE) != -1)
> if (length(w) >= 1) {
+   w <- w[1]
+   l <- l[seq(1, w-1)]
+   RcppExports.R <- file("R/RcppExports.R", "wb")
+   writeLines(l, RcppExports.R)
+   close(RcppExports.R)
+ }
> 
> .in <- suppressWarnings(readLines("src/Makevars.in"))
> .in <- gsub("@ARMA@", file.path(find.package("RcppArmadillo"),"include"), .in)
> .in <- gsub("@BH@", file.path(find.package("BH"),"include"), .in)
> .in <- gsub("@RCPP@", file.path(find.package("Rcpp"),"include"), .in)
> .in <- gsub("@EG@", file.path(find.package("RcppEigen"),"include"), .in)
> 
> .in <- gsub("@SL@", paste(capture.output(StanHeaders:::LdFlags()), capture.output(RcppParallel:::RcppParallelLibs())), #nolint
+             .in)
> 
> 
> .badStan <- ""
> .in <- gsub("@SH@", gsub("-I", "-@ISYSTEM@",
+                          paste(capture.output(StanHeaders:::CxxFlags()), # nolint
+                                capture.output(RcppParallel:::CxxFlags()), # nolint
+                                paste0("-@ISYSTEM@'", system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE), "'"),
+                                .badStan)),
+             .in)
> 
> 
> 
> if (.Platform$OS.type == "windows") {
+   .makevars <- file("src/Makevars.win", "wb")
+   .i <- "I"
+ } else {
+   .makevars <- file("src/Makevars", "wb")
+   if (any(grepl("Pop!_OS", utils::osVersion, fixed=TRUE)) ||
+           any(grepl("Ubuntu", utils::osVersion, fixed=TRUE))) {
+     .i <- "isystem"
+   } else {
+     .i <- "I"
+   }
+ }
> 
> writeLines(gsub("@ISYSTEM@", .i, .in),
+              .makevars)
> close(.makevars)
> 
> if (file.exists("man/reexports.Rd")) {
+   l <- readLines("man/reexports.Rd")
+   if (!any(regexpr("[\\]value", l) != -1)) {
+     l <- c(l, "\\value{ Inherited from parent routine }")
+     file.out <- file("man/reexports.Rd", "wb")
+     writeLines(l, file.out)
+     close(file.out)
+   }
+ }
> 
> 
> unlink("R/rxode2_md5.R")
> 
> cpp <- list.files("src", pattern = ".(c|h|cpp|f)$")
> include <- list.files("inst/include")
> #Rfiles <- list.files("R/", pattern = ".R")
> 
> cmd <- file.path(R.home("bin"), "R")
> args <- c("CMD", "config")
> 
> md5 <- digest::digest(c(lapply(c(paste0("src/", cpp),
+                                  paste0("inst/include/", include)#,
+                                  #paste0("R/", Rfiles)
+                                  ), digest::digest, file = TRUE),
+                         ## vapply(c("BLAS_LIBS", "CC",  "CFLAGS", "CPICFLAGS",
+                         ##          "CXX", "CXXFLAGS", "CXXPICFLAGS",
+                         ##          "CXX11", "CXX11STD", "CXX11FLAGS", "CXX11PICFLAGS",
+                         ##          "CXX14", "CXX14STD", "CXX14FLAGS", "CXX14PICFLAGS",
+                         ##          "CXX17", "CXX17STD", "CXX17FLAGS", "CXX17PICFLAGS",
+                         ##          "CXX20", "CXX20STD", "CXX20FLAGS", "CXX20PICFLAGS",
+                         ##          "FC", "FFLAGS", "FCFLAGS",  "FPICFLAGS"),
+                         ##        function(cfg) {
+                         ##          rawToChar(sys::exec_internal(cmd, c(args, cfg))$stdout)
+                         ##        }, character(1)
+                         ##       ),
+                         ""
+                         ))
> unlink("R/rxode2_md5.R")
> md5file <- file("R/rxode2_md5.R", "wb")
> writeLines(sprintf("rxode2.md5 <- \"%s\"\n", md5), md5file)
> close(md5file)
> 
> l <- readLines("DESCRIPTION")
> w <- which(regexpr("Version[:] *(.*)$", l) != -1)
> v <- gsub("Version[:] *(.*)$", "\\1", l[w])
> 
> unlink("inst/include/rxode2parseVer.h")
> ode.h <- file("inst/include/rxode2parseVer.h", "wb")
> writeLines(c(sprintf("#define __VER_md5__ \"%s\"", md5),
+              "#define __VER_repo__ \"https://github.com/nlmixr2/rxode2\"",
+              sprintf("#define __VER_ver__ \"%s\"", v)),
+            ode.h)
> close(ode.h)
> 
> unlink("src/sbuf.c")
> l <- readLines("inst/include/sbuf.c")
> sbuf.c <- file("src/sbuf.c", "wb")
> writeLines(l, sbuf.c)
> close(sbuf.c)
> 
> 
> unlink("src/codegen2.h")
> l <- readLines("inst/include/rxode2_model_shared.c")
> 
> l <- l[l != ""]
> l <- gsub(" *= *NULL;", "=NULL;", l)
> 
> def <- l
> w <- which(regexpr("double _prod", def) != -1) - 1
> def <- def[1:w]
> def <- gsub("=NULL", "", def)
> def <- gsub("[^ ]* *[*]?([^;]*);", "\\1", def)
> 
> def <- unique(c(def, c("_sum", "_udf", "_sign", "_prod", "_max", "_min", "_transit4P", "_transit3P", "_assignFuns0", "_assignFuns", "_getRxSolve_", "_solveData", "_rxord", "__assignFuns2")))
> 
> w0 <- which(grepl("double +_prod", l))[1]
> r <- 1:(w0 - 1)
> l0 <- l[r]
> l <- l[-r]
> 
> 
> w1 <- which(regexpr("dynamic start", l) != -1)
> l1 <- l[1:w1]
> 
> 
> 
> w2 <- which(regexpr("dynamic stop", l) != -1)
> l2 <- l[seq(w2, length(l))]
> 
> w3 <- which(regexpr("assign start", l2) != -1)
> 
> l3 <- l2[seq(w3, length(l2))]
> l2 <- l2[1:w3]
> 
> w4 <- which(regexpr("assign stop", l3) != -1)
> l3 <- l3[seq(w4, length(l3))]
> 
> dfP <- l[seq(w1+1, w2-1)]
> 
> dfP <- dfP[regexpr("^ *$", dfP)==-1]
> df <- setNames(do.call("rbind",lapply(seq_along(dfP),
+                                       function(i) {
+                                         .r <- sub("^ *", "", dfP[[i]])
+                                         .r <- sub("^([^ ]*) *= *[(]", "\\1,", .r)
+                                         .r <- sub("^([^ ]*) *[)] *R_GetCCallable *[(] *\"", "\\1,", .r, perl=TRUE)
+                                         .r <- sub("^([^ ]*) *\" *, *\"", "\\1,", .r, perl=TRUE)
+                                         .r <- sub("^([^ ]*)\" *[)] *; *", "\\1",.r, perl=TRUE)
+                                         data.frame(t(strsplit(.r, ",")[[1]]),stringsAsFactors = FALSE)
+                                       })), c("fun", "type", "package", "packageFun"))
> 
> df$rxFun <- df$fun
> df$argMax <- df$argMin <- NA_integer_
> df$threadSafe <- 1L
> df <- df[,c("rxFun", "fun", "type", "package", "packageFun", "argMin", "argMax", "threadSafe")]
> df$rxFun <- gsub("_llik", "llik", df$rxFun)
> 
> def <- def[!(def %in% df$rxFun)]
> def <- def[!(def %in% df$fun)]
> 
> .parseEnv <- new.env(parent=emptyenv())
> source("R/parseFuns.R")
> 
> df$argMin <- vapply(df$rxFun, function(f) {
+   .n <- .parseEnv$.parseNum[f]
+   if (is.na(.n)) return(NA_integer_)
+   .n <-setNames(.n, NULL)
+   as.integer(.n)
+ }, integer(1), USE.NAMES=TRUE)
> 
> df$argMax <- df$argMin
> 
> dfStr <- deparse(df)
> dfStr[1] <- paste(".parseEnv$.rxode2parseDf <- ", dfStr[1])
> 
> dfIni.R <- file("R/dfIni.R", "wb")
> writeLines(dfStr,
+            dfIni.R)
> close(dfIni.R)
> 
> ## deparse1 came from R 4.0, use deparse2
> deparse2 <- function(expr, collapse = " ", width.cutoff = 500L, ...) {
+   paste(deparse(expr, width.cutoff, ...), collapse = collapse)
+ }
> 
> final <- c("#include <time.h>",
+            "#include <stdlib.h>",
+            "unsigned long int __timeId=0;",
+            "char *genRandomChar(void);",
+            "void writeHeader(const char *md5, const char *extra) {",
+            paste0("sAppend(&sbOut, \"#define ", def, " _rx%s%s%ld_", def, "_%s\\n\", extra, md5, __timeId++, genRandomChar());"),
+            "}",
+            "void writeBody0(void) {",
+            paste0("sAppendN(&sbOut, ", vapply(paste0(l0, "\n"), deparse2, character(1)), ", ", nchar(l0) + 1, ");"),
+            "}",
+            "void writeBody1(void) {",
+            paste0("sAppendN(&sbOut, ", vapply(paste0(l1, "\n"), deparse2, character(1)), ", ", nchar(l1) + 1, ");"),
+            "}",
+            "void writeBody2(void) {",
+            paste0("sAppendN(&sbOut, ", vapply(paste0(l2, "\n"), deparse2, character(1)), ", ", nchar(l2) + 1, ");"),
+            "}",
+            "void writeBody3(void) {",
+            paste0("sAppendN(&sbOut, ", vapply(paste0(l3, "\n"), deparse2, character(1)), ", ", nchar(l3) + 1, ");"),
+            "}",
+            "void writeFooter(void) {",
+            paste0("sAppendN(&sbOut, \"#undef ", def, "\\n\", ", nchar(def) + 8, ");"),
+            "}"
+            )
> 
> codegen2.h <- file("src/codegen2.h", "wb")
> writeLines(final,
+            codegen2.h)
> close(codegen2.h)
> 
> proc.time()
   user  system elapsed 
   0.54    0.20    0.68 
